Paul Adams Publications

2024
  1. Cowie AE, Pereira JH, DeGiovanni A, McAndrew RP, Palayam M, Peek JO, Muchlinski AJ, Yoshikuni Y, Shabek N, Adams PD, Zerbe: The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity. J. Biol. Chem. 2024, [online ahead of print] [PMID: 39454950] [PMCID: ]

  2. Gupta K, Tian Y, Eudes A, Scheller HV, Singh AK, Adams PD, Andeer PF, Northen TR: EcoFAB 3.0: a sterile system for studying sorghum that replicates previous field and greenhouse observations. Front Plant Sci. 2024, 15:1440728. [PMID: 39435021] [PMCID: PMC11491363]

  3. Rodrigues AV, Moriarty NW, Kakumanu R, DeGiovanni A, Pereira JH, Gin JW, Chen Y, Baidoo EEK, Petzold CJ, Adams PD: Characterization of lignin degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid (PDC). J. Biol. Chem. 2024, [online ahead of print] [PMID: 39222681] [PMCID: PMC11489326]

  4. Sirirungruang S, Blay V, Scott YF, Pereira JH, Hammel M, Barnum CR, Adams PD, Shih PM: Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1. J. Biol. Chem. 2024, 300:107602 [PMID: 39059496] [PMCID: PMC11381871]

  5. Read RJ, Pettersen EF, McCoy AJ, Croll TI, Terwilliger TC, Poon BK, Meng EC, Liebschner D, Adams PD: Likelihood-based interactive local docking into cryo-EM maps in ChimeraX. Acta Cryst. 2024, 80:588-598. [PMID: 39058381] [PMCID: PMC11301754]

  6. Moriarty NW, Moussa J, Adams PD: Protonation of histidine rings using quantum-mechanical methods. Acta Cryst. 2024, 80:639-646. [PMID: 39052316] [PMCID: PMC11301759]

  7. Yunus IS, Hudson GA, Chen Y, Gin JW, Kim J, Baidoo EEK, Petzold CJ, Adams PD, Simmons BA, Mukhopadhyay A, Keasling JD, Lee TS: Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida. Metab. Eng. 2024, 84:69-82. [PMID: 38839037] [PMCID: ]

  8. Zhang Y, Sharma D, Liang Y, Downs N, Dolman F, Thorne K, Black IM, Pereira JH, Adams P, Scheller HV, O'Neill M, Urbanowicz B, Mortimer JC: Putative rhamnogalacturonan-II glycosyltransferase identified through callus gene editing bypasses embryo lethality. Plant Physiol. 2024, 195:2551-2565. [PMID: 38739546] [PMCID: PMC11288761]

  9. Poon BK, Terwilliger TC, Adams PD: The Phenix-AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix. Proteins 2024, 33:e4992. [PMID: 38647406] [PMCID: PMC11034488]

  10. Pham LTM, Deng K, Choudhary H, Northen TR, Singer SW, Adams PD, Simmons BA, Sale KL: An Engineered Laccase from Fomitiporia mediterranea Accelerates Lignocellulose Degradation. Biomolecules 2024, 14:324. [PMID: 38540744] [PMCID: PMC10968408]

  11. Urzhumtsev AG, Adams PD, Afonine PV: Universal parameters of bulk-solvent masks. Acta Cryst. 2024, A80: [PMID: ] [PMCID: ]

  12. Banerjee D, Yunus IS, Wang X, Kim J, Srinivasan A, Menchavez R, Chen Y, Gin JW, Petzold CJ, Martin HG, Magnuson JK, Adams PD, Simmons BA, Mukhopadhyay A, Kim J, Lee TS: Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida. Metab Eng. 2024, 82:157-170. [PMID: 38369052] [PMCID: ]

  13. Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schröder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S: Community recommendations on cryoEM data archiving and validation IUCrJ 2024, 11:140-151. [PMID: 38358351] [PMCID: PMC10916293]

  14. Afonine PV, Adams PD, Sobolev OV, Urzhumtsev AG: Accounting for nonuniformity of bulk-solvent: A mosaic model. Protein Sci. 2024, 33:e4909. [PMID: 38358136] [PMCID: PMC10868464]

  15. Environmental stress mediates groundwater microbial community assembly. Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J: Environmental stress mediates groundwater microbial community assembly. Nat Microbiol. 2024, 9:490-501. [PMID: 38212658] [PMCID: ]

  16. Terwilliger TC, Liebschner D, Croll TI, Williams CJ, McCoy AJ, Poon BK, Afonine PV, Oeffner RD, Richardson JS, Read RJ, Adams PD: AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination. Nature Methods 2024, 21:110-116. [PMID: 38036854] [PMCID: PMC10776388]

2023
  1. Liebschner D, Afonine PV, Poon BK, Moriarty NW, Adams PD: Improved joint X-ray and neutron refinement procedure in Phenix. Acta Cryst. 2023, 79:1079-1093. [PMID: 37942718] [PMCID: PMC10833352]

  2. Shrestha S, Awasthi D, Chen Y, Gin J, Petzold CJ, Adams PD, Simmons BA, Singer SW: Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2 Appl Environ Microbiol. 2023, 89:e0085223. [PMID: 37724856] [PMCID: PMC10617552]

  3. Afonine PV, Sobolev OV, Moriarty NW, Terwilliger TC, Adams PD: Overall protein structure quality assessment using hydrogen-bonding parameters. Acta Cryst. 2023, 79:684-693. [PMID: 37431759] [PMCID: PMC10394671]

  4. Chen Y, Gin JW, Wang Y, de Raad M, Tan S, Hillson NJ, Northen TR, Adams PD, Petzold CJ: Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format. PLoS One 2023, 18:e0288102. [PMID: 37418444] [PMCID: PMC10328223]

  5. Takasuka T, Kim H, Deng K, Bianchetti CM, Yamashita K, Beebe ET, Bergeman LF, Vander Meulen KA, Deutsch S, Ralph J, Adams PD, Northen TR, Fox BG: Quantitative analysis of The High Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase. Chembiochem 2023, 24:e202300357. [PMID: 37402642] [PMCID: ]

  6. Ha NS, Onley JR, Deng K, Andeer P, Bowen BP, Gupta K, Kim PW, Kuch N, Kutschke M, Parker A, Song F, Fox B, Adams PD, de Raad M, Northen TR: A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening. Lab Chip 2023, 23:3361-3369 [PMID: 37401915] [PMCID: PMC10484474]

  7. Afonine PV, Adams PD, Urzhumtsev AG: Efficient structure-factor modeling for crystals with multiple components. Acta Cryst. 2023, A79:345-352. [PMID: 37338214] [PMCID: PMC10317137]

  8. Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK: Structural evidence for intermediates during O2 formation in photosystem II. Nature 2023, 617:629-636. [PMID: 37138085] [PMCID: PMC10191843]

  9. Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD: Complete integration of carbene-transfer chemistry into biosynthesis. Nature 2023, 617:403-408. [PMID: 37138074] [PMCID: ]

  10. Englund E, Schmidt M, Nava AA, Lechner A, Deng K, Jocic R, Lin Y, Roberts J, Benites VT, Kakumanu R, Gin JW, Chen Y, Liu Y, Petzold CJ, Baidoo EEK, Northen TR, Adams PD, Katz L, Yuzawa S, Keasling JD: Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase. J Am Chem Soc. 2023, 145:8822-8832. [PMID: 37057992] [PMCID: PMC10141241]

  11. Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, Phillips L, Rainville C, Sterner DE, Kumaran D, Andi B, Babnigg G, Moriarty NW, Adams PD, Joachimiak A, Hurst BL, Kumar S, Butt TR, Jonsson CB, Ferrins L, Wakatsuki S, Galanie S, Head MS, Parks JM: Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nature Comm. 2023, 14:1733. [PMID: 36977673] [PMCID: PMC10044120]

  12. Terwilliger TC, Afonine PV, Liebschner D, Croll TI, McCoy AJ, Oeffner RD, Williams CJ, Poon BK, Richardson JS, Read RJ, Adams PD: Accelerating crystal structure determination with iterative AlphaFold prediction. Acta Cryst. 2023, D79:234-244. [PMID: 36876433] [PMCID: PMC9986801]

  13. Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR: Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. Nature Plants 2023, 9:486-500. [PMID: 36849618] [PMCID: PMC10115243]

  14. Dai J, Wilhelm KB, Bischoff AJ, Pereira JH, Dedeo MT, García-Almedina DM, Adams PD, Groves JT, Francis MB: A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins Small 2023, 19:e2207805. [PMID: 36811150] [PMCID: ]

  15. Liebschner D, Moriarty NW, Poon BK, Adams PD: In situ ligand restraints from quantum-mechanical methods. Acta Cryst. 2023, D79:100-110 [PMID: 36762856] [PMCID: PMC9912925]

  16. Bloomer BJ, Natoli SN, Garcia-Borràs M, Pereira JH, Hu DB, Adams PD, Houk KN, Clark DS, Hartwig JF: Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics. Nature Catalysis 2023, 6:39-51 [PMID: ] [PMCID: ]

  17. Deng K, Wang X, Ing N, Opgenorth P, de Raad M, Kim J, Simmons BA, Adams PD, Singh AK, Lee TS, Northen TR: Rapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS) Anal Biochem. 2023, 662:114997 [PMID: 36435200] [PMCID: Free article]

2022
  1. Tom LM, Aulitto M, Wu YW, Deng K, Gao Y, Xiao N, Rodriguez BG, Louime C, Northen TR, Eudes A, Mortimer JC, Adams PD, Scheller HV, Simmons BA, Ceja-Navarro JA, Singer SW: Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. Microbiome 2022, 10:183 [PMID: 36280858] [PMCID: PMC9594917]

  2. Terwilliger TC, Poon BK, Afonine PV, Schlicksup CJ, Croll TI, Millán C, Richardson JS, Read RJ, Adams PD: Improved AlphaFold modeling with implicit experimental information. Nature Methods 2022, 19:1376-1382. [PMID: 36266465] [PMCID: PMC9636017]

  3. Liu AK, Pereira JH, Kehl AJ, Rosenberg DJ, Orr DJ, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM: Structural plasticity enables evolution and innovation of RuBisCO assemblies. Sci. Adv. 2022, 8:eadc9440 [PMID: 36026446] [PMCID: PMC9417184]

  4. Andi B, Kumaran D, Kreitler DF, Soares AS, Keereetaweep J, Jakoncic J, Lazo EO, Shi W, Fuchs MR, Sweet RM, Shanklin J, Adams PD, Schmidt JG, Head MS, McSweeney S: Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Sci. Rep. 2022, 12:12197 [PMID: 35842458] [PMCID: PMC9287821]

  5. Macdonald SS, Pereira JH, Liu F, Tegl G, DeGiovanni A, Wardman JF, Deutsch S, Yoshikuni Y, Adams PD, Withers SG: A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β-Linked GlcNAc Polysaccharides. ACS Central Science 2022, 8:430-440 [PMID: 35505869] [PMCID: PMC9052796]

  6. Westbrook JD, Young JY, Shao C, Feng Z, Guranovic V, Lawson CL, Vallat B, Adams PD, Berrisford JM, Bricogne G, Diederichs K, Joosten RP, Keller P, Moriarty NW, Sobolev OV, Velankar S, Vonrhein C, Waterman DG, Kurisu G, Berman HM, Burley SK, Peisach E: PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology. J Mol Biol. 2022, 434:167599 [PMID: 35460671] [PMCID: Free article]

  7. Iwai K, Wehrs M, Garber M, Sustarich J, Washburn L, Costello Z, Kim PW, Ando D, Gaillard WR, Hillson NJ, Adams PD, Mukhopadhyay A, Garcia Martin H, Singh AK: Scalable and automated CRISPR-based strain engineering using droplet microfluidics. Microsyst Nanoeng. 2022, 8:31 [PMID: 35359611] [PMCID: PMC8924257]

  8. Chen Y, Kaplan Lease N, Gin JW, Ogorzalek TL, Adams PD, Hillson NJ, Petzold CJ: Modular automated bottom-up proteomic sample preparation for high-throughput applications. PLoS One 2022, 17:e0264467 [PMID: 35213656] [PMCID: PMC8880914]

  9. Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A: Integration of software tools for integrative modeling of biomolecular systems. J. Struct. Biol. 2022, 214:107841 [PMID: 35149213] [PMCID: PMC9278553]

2021
  1. Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J: Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition. Nature Communications 2021, 12:6531. [PMID: 34764256] [PMCID: PMC8585918]

  2. Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, Pereira JH, Rodrigues AV, van Dijk AA, Ebrecht AC, Opperman DJ, Sagmeister T, Buhlheller C, Pavkov-Keller T, Rathinaswamy MK, Dalwadi U, Yip CK, Burke JE, Garcia KC, Grishin NV, Adams PD, Read RJ, Baker D: Accurate prediction of protein structures and interactions using a three-track neural network. Science 2021, 373:871-876. [PMID: 34282049] [PMCID: PMC7612213]

  3. Ibrahim M, Moriarty NW, Kern J, Holton JM, Brewster AS, Bhowmick A, Bergmann U, Zouni A, Messinger J, Yachandra VK, Yano J, Dobbek H, Sauter NK, Adams PD: Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map. Proc Natl Acad Sci U S A. 2021, 118:e2102342118. [PMID: 34117122] [PMCID: PMC8214684]

  4. Ing N, Deng K, Chen Y, Aulitto M, Gin JW, Pham TLM, Petzold CJ, Singer SW, Bowen B, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR: A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities. Scientific Reports 2021, 11:11803. [PMID: 34083602] [PMCID: PMC8175421]

  5. Pham LTM, Deng K, Northen TR, Singer SW, Adams PD, Simmons BA, Sale KL: Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium. Biotechnol Biofuels. 2021, 14:108 [PMID: 33926536] [PMCID: PMC8082889]

  6. Lui LM, Majumder EL, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP: Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol. 2021, 12:642422 [PMID: 33841364] [PMCID: PMC8024649]

  7. Terwilliger TC, Sobolev OV, Afonine PV, Adams PD, Ho CM, Li X, Zhou ZH: Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching. Acta Cryst. 2021, D77:457-462 [PMID: 33825706] [PMCID: PMC8025881]

  8. van Zundert GCP, Moriarty NW, Sobolev OV, Adams PD, Borrelli KW: Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. Structure 2021, 29:913-921.e4 [PMID: 33823127] [PMCID: PMC8349848]

  9. Teze D, Coines J, Fredslund F, Dubey KD, Bidart GN, Adams PD, Dueber JE, Svensson B, Rovira C, Welner DH: O-/N-/S-Specificity in Glycosyltransferase Catalysis: From Mechanistic Understanding to Engineering. ACS Catalysis 2021, 11:1810-1815. [PMID: ] [PMCID: ]

  10. Kim J, Baidoo EEK, Amer B, Mukhopadhyay A, Adams PD, Simmons BA, Lee TS: Engineering Saccharomyces cerevisiae for isoprenol production. Metab Eng. 2021, 64:154-166. [PMID: 33581331] [PMCID: ]

  11. Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA Jr, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W: Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Meth. 2021, 18:156-164. [PMID: 33542514] [PMCID: PMC7864804]

  12. Wang X, Pereira JH, Tsutakawa S, Fang X, Adams PD, Mukhopadhyay A, Lee TS: Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450. Metab. Eng. 2021, 64:41-51. [PMID: 33482331] [PMCID: PMC7987753]

  13. Liebschner D, Afonine PV, Moriarty NW, Poon BK, Chen VB, Adams PD: CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. Acta Cryst. 2021, D77:48-61. [PMID: 33404525] [PMCID: PMC7787109]

2020
  1. Moriarty NW, Liebschner D, Tronrud DE, Adams PD: Arginine off-kilter: guanidinium is not as planar as restraints denote. Acta Cryst. 2020, D76:1159-1166. [PMID: 33263321] [PMCID: PMC7709202]

  2. Ge X, Thorgersen MP, Poole FL 2nd, Deutschbauer AM, Chandonia JM, Novichkov PS, Gushgari-Doyle S, Lui LM, Nielsen T, Chakraborty R, Adams PD, Arkin AP, Hazen TC, Adams MWW: Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. Front Microbiol. 2020, 11:587127. [PMID: 33193240] [PMCID: PMC7604516]

  3. Ge X, Thorgersen MP, Poole FL 2nd, Deutschbauer AM, Chandonia JM, Novichkov PS, Adams PD, Arkin AP, Hazen TC, Adams MWW: Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. Microbiol Resour Announc. 2020, 9:e01149-20. [PMID: 33122416] [PMCID: PMC7595952]

  4. Terwilliger TC, Sobolev OV, Afonine PV, Adams PD, Read RJ: Density modification of cryo-EM maps. Acta Cryst. 2020, D76:912-925. [PMID: 33021493] [PMCID: PMC7543659]

  5. Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E, Adams PD, Banfield JF, Shih PM: Novel bacterial clade reveals origin of form I Rubisco. Nature Plants 2020, 6:1158-1166. [PMID: 32868887] [PMCID: ]

  6. Sobolev OV, Afonine PV, Moriarty NW, Hekkelman ML, Joosten RP, Perrakis A, Adams PD: A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. Structure 2020, 28:1249-1258.e2. [PMID: 32857966] [PMCID: PMC7642142]

  7. Terwilliger TC, Ludtke SJ, Read RJ, Adams PD, Afonine PV: Improvement of cryo-EM maps by density modification. Nature Methods 2020, 9:923-927. [PMID: 32807957] [PMCID: PMC7484085]

  8. Thompson MG, Blake-Hedges JM, Pereira JH, Hangasky JA, Belcher MS, Moore WM, Barajas JF, Cruz-Morales P, Washington LJ, Haushalter RW, Eiben CB, Liu Y, Skyrud W, Benites VT, Barnum TP, Baidoo EEK, Scheller HV, Marletta MA, Shih PM, Adams PD, Keasling JD: An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism. Nat Commun. 2020, 11:2931. [PMID: 32523014] [PMCID: PMC7286885]

  9. Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J: Untangling the sequence of events during the S2 ➔ S3 transition in photosystem II and implications for the water oxidation mechanism. Proc Natl Acad Sci U S A. 2020, 117:12624-12635. [PMID: 32434915] [PMCID: PMC7293653]

  10. Curran SC, Pereira JH, Baluyot MJ, Lake J, Puetz H, Rosenburg DJ, Adams P, Keasling JD: Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster. Biochemistry 2020, 59:1630-1639. [PMID: 32250597] [PMCID: ]

  11. Park MR, Chen Y, Thompson M, Benites VT, Fong B, Petzold CJ, Baidoo EEK, Gladden JM, Adams PD, Keasling JD, Simmons BA, Singer SW: Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass. ChemSusChem. 2020, 13:4455-4467. [PMID: 32160408] [PMCID: ]

  12. Liebschner D, Afonine PV, Moriarty NW, Adams PD: What Are the Current Limits on Determination of Protonation State Using Neutron Macromolecular Crystallography? Methods Enzymol. 2020, 634:225-255 [PMID: 32093835] [PMCID: PMC7571246]

  13. Liebschner D, Afonine PV, Urzhumtsev AG, Adams PD: Implementation of the Riding Hydrogen Model in CCTBX to Support the Next Generation of X-ray and Neutron Joint Refinement in Phenix. Methods Enzymol. 2020, 634:177-199 [PMID: 32093832] [PMCID: PMC7574815]

  14. Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, Adams PD: Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Acta Cryst. 2020, D76:51-62 [PMID: 31909743] [PMCID: PMC6939439]

  15. Blake-Hedges JM, Pereira JH, Cruz-Morales P, Thompson MG, Barajas JF, Chen J, Krishna RN, Chan LJG, Nimlos D, Alonso-Martinez C, Baidoo EEK, Chen Y, Gin JW, Katz L, Petzold CJ, Adams PD, Keasling JD: Structural mechanism of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase. J Am Chem Soc. 2020, 142:835-846. [PMID: 31793780] [PMCID: Free article]

  16. Terwilliger TC, Adams PD, Afonine PV, Sobolev OV: Cryo-EM map interpretation and protein model-building using iterative map segmentation. Protein Sci. 2020, 29:87-99. [PMID: 31599033] [PMCID: PMC6933853]

2019
  1. Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN Jr, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A: Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 2019, 27:1745-1759. [PMID: 31780431] [PMCID: PMC7108332]

  2. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Cryst. 2019, D75:861-877 [PMID: 31588918] [PMCID: PMC6778852]

  3. Kang A, Mendez-Perez D, Goh EB, Baidoo EEK, Benites VT, Beller HR, Keasling JD, Adams PD, Mukhopadhyay A, Lee TS: Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli. Metab Eng. 2019, 56:85-96 [PMID: 31499175] [PMCID: ]

  4. Chen Y, Guenther JM, Gin JW, Chan LJG, Costello Z, Ogorzalek TL, Tran HM, Blake-Hedges JM, Keasling JD, Adams PD, García Martín H, Hillson NJ, Petzold CJ: Automated "Cells-To-Peptides" Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes. J Proteome Res. 2019, 18:3752-3761 [PMID: 31436101] [PMCID: Free article]

  5. Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K: Cryo_fit: Democratization of flexible fitting for cryo-EM. J Struct Biol. 2019, 208:1-6 [PMID: 31279069] [PMCID: PMC7112765]

  6. Barajas JF, McAndrew RP, Thompson MG, Backman TWH, Pang B, de Rond T, Pereira JH, Benites VT, Martín HG, Baidoo EEK, Hillson NJ, Adams PD, Keasling JD: Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases. J Ind Microbiol Biotechnol. 2019, 46:1225-1235 [PMID: 31115703] [PMCID: PMC6697708]

  7. Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD: Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism. MBio 2019, 10:e02577-18 [PMID: 31064836] [PMCID: PMC6509195]

  8. Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY: Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Cryst. 2019, D75:451-454. [PMID: 30988261] [PMCID: PMC6465986]

  9. Dong J, Chen Y, Benites VT, Baidoo EEK, Petzold CJ, Beller HR, Eudes A, Scheller HV, Adams PD, Mukhopadhyay A, Simmons BA, Singer SW: Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids. Biotechnol Bioeng. 2019, 116:1909-1922 [PMID: 30982958] [PMCID: ]

  10. Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, Keasling JD, Adams PD, Petzold CJ: A rapid methods development workflow for high-throughput quantitative proteomic applications. PLoS One 2019, 14:e0211582. [PMID: 30763335] [PMCID: PMC6375547]

  11. Ge X, Vaccaro BJ, Thorgersen MP, Poole FL 2nd, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW: Iron- and Aluminum-Induced Depletion of Molybdenum in Acidic Environments Impedes the Nitrogen Cycle. Environ Microbiol. 2019, 21:152-163. [PMID: 30289197] [PMCID: Free article]

  12. Moriarty NW, Adams PD: Iron-sulfur clusters have no right angles. Acta Cryst. 2019, D75:16-20. [PMID: 30644841] [PMCID: PMC6333285]

2018
  1. Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK: Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature 2018, 563:421-425. [PMID: 30405241] [PMCID: PMC6485242]

  2. Liu CL, Tian T, Alonso-Gutierrez J, Garabedian B, Wang S, Baidoo EEK, Benites V, Chen Y, Petzold CJ, Adams PD, Keasling JD, Tan T, Lee TS: Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli. Biotechnol Biofuels 2018, 11:285 [PMID: 30377444] [PMCID: PMC6195743]

  3. Terwilliger TC, Adams PD, Afonine PV, Sobolev OV: A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. Nat Methods 2018, 15:905-908. [PMID: 30377346] [PMCID: PMC6214191]

  4. Deng K, Zeng J, Cheng G, Gao J, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR: Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS). Biotechnol Biofuels 2018, 11:266. [PMID: 30275906] [PMCID: PMC6158898]

  5. Kryshtafovych A, Monastyrskyy B, Adams PD, Lawson CL, Chiu W: Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge. Data Brief 2018, 20:1629-1638. [PMID: 30263915] [PMCID: PMC6157618]

  6. Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A: New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Cryst. 2018, D74:814-840. [PMID: 30198894] [PMCID: PMC6130467]

  7. Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP: Jungle Express is a versatile repressor system for tight transcriptional control. Nature Comm. 2018, 9:3617 [PMID: 30190458] [PMCID: PMC6127294]

  8. Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD: Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Acta Cryst. 2018, D74:800-813. [PMID: 30082516] [PMCID: PMC6079631]

  9. Terwilliger TC, Adams PD, Afonine PV, Sobolev OV: Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. J. Struct. Biol. 2018, 204:338-343 [PMID: 30063987] [PMCID: PMC6163059]

  10. Kryshtafovych A, Adams PD, Lawson CL, Chiu W: Evaluation system and web infrastructure for the second cryo-EM model challenge. J. Struct. Biol. 2018, 204:96-108 [PMID: 30017700] [PMCID: PMC6205695]

  11. Ellinghaus TL, Pereira JH, McAndrew RP, Welner DH, DeGiovanni AM, Guenther JM, Tran HM, Feldman T, Simmons BA, Sale KL, Adams PD: Engineering glycoside hydrolase stability by the introduction of zinc binding. Acta Cryst 2018, D74:702-710. [PMID: 29968680] [PMCID: PMC6038386]

  12. Afonine PV, Adams PD, Urzhumtsev A: From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. Acta Cryst 2018, D74:621-631. [PMID: 29968672] [PMCID: PMC6038382]

  13. Terwilliger TC, Sobolev OV, Afonine PV, Adams PD: Automated map sharpening by maximization of detail and connectivity. Acta Cryst 2018, D74:545-559. [PMID: 29872005] [PMCID: PMC6096490]

  14. Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD: Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst 2018, D74:531-544. [PMID: 29872004] [PMCID: PMC6096492]

  15. Beller HR, Rodrigues AV, Zargar K, Wu Y-W, Saini AV, Saville RM, Pereira JH, Adams PD, Tringe SG, Petzold CJ, Keasling JD: Discovery of enzymes for toluene synthesis from anoxic microbial communities. Nature Chem. Bio. 2018, 14:451-457. [PMID: 29556105] [PMCID: ]

  16. George KW, Thompson M, Kim J, Baidoo EEK, Wang G, Benites VT, Petzold CJ, Chan LJG, Yilmaz S, Turhanen P, Adams PD, Keasling JD, Lee TS: Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli. Metab. Eng. 2018, 47:60-72. [PMID: 29530749] [PMCID: ]

  17. Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM: DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs J. Appl. Cryst. 2018, 51:193-199 [PMID: 29507550] [PMCID: PMC5822993]

  18. He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J: Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning. mBio 2018, 9:e02435-17 [PMID: 29463661] [PMCID: PMC5821090]

  19. Hsu TM, Welner DH, Russ ZN, Cervantes B, Prathuri RL, Adams PD, Dueber JE: Employing a biochemical protecting group for a sustainable indigo dyeing strategy. Nature Chem. Biol. 2018, 14:256-261 [PMID: 29309053] [PMCID: PMC5866135]

  20. Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW: A bacterial pioneer produces cellulase complexes that persist through community succession. Nature Microbiol. 2018, 3:99-107 [PMID: 29109478] [PMCID: PMC6794216]

  21. Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC: MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018, 27:293-315 [PMID: 29067766] [PMCID: PMC5734394]

  22. Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd J, Poon BK, Adams PD: Interactive Comparison and Remediation of Collections of Macromolecular Structures. Protein Sci. 2018, 27:182-194 [PMID: 28901593] [PMCID: PMC5734393]

2017
  1. Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams PD, Sale KL, Simmons BA, Baker SE, Magnuson JK, Gladden JM: Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. PLoS One 2017, 12:e0189604 [PMID: 29281693] [PMCID: PMC5744941]

  2. Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS: Towards industrial production of isoprenoids in Escherichia coli: lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnol Bioeng. 2017, 115:1000-1013 [PMID: 29278415] [PMCID: Free article]

  3. Greber BJ, Nguyen THD, Fang J, Afonine PV, Adams PD, Nogales E: The cryo-electron microscopy structure of human transcription factor IIH. Nature 2017, 549:414-417 [PMID: 28902838] [PMCID: PMC5844561]

  4. Sauter NK, Adams PD: Overcoming Data Processing Challenges for Breakthrough Crystallography. in X-Ray Free Electron Lasers: Applications in Materials, Chemistry and Biology. Eds. Bergmann U, Yachandra V, Yano J. The Royal Society of Chemistry. 2017, 70-87.

  5. Pereira JH, McAndrew RP, Tomaleri GP, Adams PD: Berkeley Screen: a set of 96 solutions for general macromolecular crystallization. J. Appl. Cryst. 2017, 50:1352-1358. [PMID: 29021733] [PMCID: PMC5627680]

  6. Morrell W, Birkel G, Forrer M, Lopez T, Backman T, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso Gutierrez J, George K, Mukhopadhyay A, Vaino I, Keasling JD, Adams PD, Hillson NJ, Garcia Martin H: The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization. ACS Synth Biol. 2017, 6:2248-2259 [PMID: 28826210] [PMCID: ]

  7. McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD: Reply to Kiser: Dioxygen binding in NOV1 crystal structures. Proc Natl Acad Sci U S A 2017, 114:E6029-E6030 [PMID: 28679635] [PMCID: PMC5544338]

  8. Pereira JH, McAndrew RP, Sergeeva OA, Ralston CY, King JA, Adams PD: Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy. Sci. Rep. 2017, 16:3673 [PMID: 28623285] [PMCID: PMC5473854]

  9. Welner DH, Shin D, Tomaleri GP, DeGiovanni AM, Tsai AY, Tran HM, Hansen SF, Green DT, Scheller HV, Adams PD: Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes. PLoS One 2017, 12:e0177591 [PMID: 28598995] [PMCID: PMC5466300]

  10. Kohler AC, Mills MJL, Adams PD, Simmons BA, Sale KL: Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism. Proc Natl Acad Sci U S A 2017, 114:E3205-E3214 [PMID: 28373573] [PMCID: PMC5402402]

  11. Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EE, Wang G, Chan LJ, Adams PD, Petzold CJ, Keasling JD, Lee TS: Production of jet fuel precursor monoterpenoids from engineered Escherichia coli. Biotechnol Bioeng. 2017, 114:1703-1712 [PMID: 28369701] [PMCID: Free article]

  12. Welner DH, Tsai AY, DeGiovanni AM, Scheller HV, Adams PD: X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa. Acta Cryst 2017, F73:241-245. [PMID: 28368284] [PMCID: PMC5379175]

  13. Hryc CF, Chen DH, Afonine PV, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams PD, King JA, Schmid MF, Chiu W: Accurate model annotation of a near-atomic resolution cryo-EM map. Proc Natl Acad Sci U S A 2017, 114:3103-3108. [PMID: 28270620] [PMCID: PMC5373346]

  14. Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD: Polder maps: improving OMIT maps by excluding bulk solvent. Acta Cryst. 2017, D73:148-157 [PMID: 28177311] [PMCID: PMC5297918]

  15. Moriarty NW, Draizen EJ, Adams PD: An editor for the generation and customization of geometry restraints. Acta Cryst. 2017, D73:123-130 [PMID: 28177308] [PMCID: PMC5297915]

  16. Heinemann J, Deng K, Shih SC, Gao J, Adams PD, Singh AK, Northen TR: On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening. Lab Chip 2017, 17:323-331 [PMID: 27957569] [PMCID: ]

  17. Yuzawa S, Deng K, Wang G, Baidoo EE, Northen TR, Adams PD, Katz L, Keasling JD: Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production. ACS Synth. Biol. 2017, 6:139-147 [PMID: 27548700] [PMCID: ]

2016
  1. McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD: Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase. Proc Natl Acad Sci U S A 2016, 113:14324-14329 [PMID: 27911781] [PMCID: PMC5167157]

  2. Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller FD, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Vo Pham L, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J: Structure of photosystem II and substrate binding at room temperature. Nature 2016, 540:453-457 [PMID: 27871088] [PMCID: PMC5201176]

  3. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD: From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum. Acta Cryst. 2016, D72:1073-1075 [PMID: 27599739] [PMCID: PMC5013599]

  4. Janowski PA, Moriarty NW, Kelley BP, Case DA, York DM, Adams PD, Warren GL: Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Cryst. 2016, D72:1062-7 [PMID: 27599738] [PMCID: PMC5013598]

  5. Hiras J, Wu YW, Deng K, Nicora CD, Aldrich JT, Frey D, Kolinko S, Robinson EW, Jacobs JM, Adams PD, Northen TR, Simmons BA, Singer SW: Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis. MBio 2016, 2:e01106-16 [PMID: 27555310] [PMCID: PMC4999548]

  6. Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, Keasling JD, Palsson BO, Lee TS: Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Syst. 2016, 2:335-46 [PMID: 27211860] [PMCID: PMC4882250]

  7. Sauter NK, Echols N, Adams PD, Zwart PH, Kern J, Brewster AS, Koroidov S, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Yano J, Yachandra VK: No observable conformational changes in PSII. Nature 2016, 533:E1-2 [PMID: 27193689] [PMCID: PMC6020672]

  8. Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J: Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure 2016, 24:502-8 [PMID: 27050687] [PMCID: PMC5070601]

  9. Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD: Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-aryl Ether Cleavage Pathway from Sphingobium sp SYK-6. J Biol Chem. 2016, 291:10228-38 [PMID: 26940872] [PMCID: PMC4858972]

  10. Terwilliger TC, Bunkóczi G, Hung L-W, Zwart PH, Smith JL, Akey DL, Adams PD: Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal Acta Cryst. 2016, 72:359-374 [PMID: 26960123] [PMCID: PMC4784667]

  11. Terwilliger TC, Bunkóczi G, Hung L-W, Zwart PH, Smith JL, Akey DL, Adams PD: Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing Acta Cryst. 2016, 72:346-358 [PMID: 26960122] [PMCID: PMC4784666]

  12. Moriarty NW, Tronrud DE, Adams PD, Karplus PA: A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream Acta Cryst. 2016, 72:176-179 [PMID: 26894545] [PMCID: PMC4756615]

  13. Eudes A, Pereira JH, Yogiswara S, Wang G, Teixeira Benites V, Baidoo EE, Lee TS, Adams PD, Keasling JD, Loqué D: Exploiting The Substrate Promiscuity of Hydroxycinnamoyl-CoA:shikimate Hydroxycinnamoyl Transferase to Reduce Lignin. Plant Cell Physiol. 2016, 57:568-79 [PMID: 26858288] [PMCID: PMC4790474]

  14. Gach PC, Shih SC, Sustarich J, Keasling JD, Hillson NJ, Adams PD, Singh AK: A Droplet Microfluidic Platform for Automating Genetic Engineering. ACS Synthetic Biology 2016, 5426-433 [PMID: 26830031] [PMCID: Free article]

  15. Sun L, Singh S, Joo M, Vega-Sanchez M, Ronald P, Simmons BA, Adams P, Auer M: Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy. Biotechnol Bioeng. 2016, 113:82-90 [PMID: 26137889] [PMCID: ]

2015
  1. Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG: Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. Biotechnol Biofuels 2015, 8:220 [PMID: 26697109] [PMCID: PMC4687162]

  2. Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP Jr, Bingman CA, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN Jr: Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin. J Biol Chem. 2015, 291:5234-46 [PMID: 26637355] [PMCID: PMC4777856]

  3. Schwessinger B, Li X, Ellinghaus TL, Chan LJ, Wei T, Joe A, Thomas N, Pruitt R, Adams PD, Chern MS, Petzold CJ, Liu CC, Ronald PC: A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection. Integrative Biology 2015, 8:542-5 [PMID: 26611838] [PMCID: PMC5061041]

  4. Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG: Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol 2015, 3:165 [PMID: 26579511] [PMCID: PMC4621489]

  5. Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR: Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol 2015, 3:153 [PMID: 26528471] [PMCID: PMC4603251]

  6. Petzold CJ, Chan LJ, Nhan M, Adams PD: Analytics for Metabolic Engineering. Front Bioeng Biotechnol 2015, 3:135 [PMID: 26442249] [PMCID: PMC4561385]

  7. Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS: EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nature Methods 2015, 12:943-6 [PMID: 26280328] [PMCID: PMC4589481]

  8. Zwart P, Taylor J, Morton S, Cayford R, Fontenay G, Allaire M, Sankaran B, Dickert J, Royal K, Rozales A, Dauz A, Bryant D, Smith N, Ortega S, Sauter N, Adams P, Ralston C: The Berkeley Center for Structural Biology at the Advanced Light Source. Synchrotron Radiation News 2015, 28, 2:22-27.

  9. Afonine PV, Urzhumtsev A, Adams PD: Macromolecular crystallographic structure refinement. in Arbor, Celebrating 100 years of modern crystallography 2015, 191:a219

  10. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD: From deep TLS validation to ensembles of atomic models built from elemental motions. Acta Cryst. 2015, 71:1668-83 [PMID: 26249348] [PMCID: PMC4528800]

  11. Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS: Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Cryst. 2015, 71:1657-67 [PMID: 26249347] [PMCID: PMC4528799]

  12. Sobolev OV, Afonine PV, Adams PD, Urzhumtsev A: Programming new geometry restraints: parallelity of atomic groups. J. Appl .Cryst. 2015, 48:1130-1141 [PMID: 26306091] [PMCID: PMC4520290]

  13. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD: Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 2015, 23:1156-67 [PMID: 26095030] [PMCID: PMC4933300]

  14. Shih SC, Goyal G, Kim PW, Koutsoubelis N, Keasling JD, Adams PD, Hillson NJ, Singh AK: A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synth Biol. 2015, 4:1151-64 [PMID: 26075958] [PMCID: Free article]

  15. George KW, Thompson MG, Kang A, Baidoo E, Wang G, Chan LJ, Adams PD, Petzold CJ, Keasling JD, Soon Lee T: Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli. Sci Rep. 2015, 5:11128. [PMID: 26052683] [PMCID: PMC4459108]

  16. Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW: NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat. Struct. Mol. Biol. 2015, 22:433-4. [PMID: 26036565] [PMCID: PMC4546829]

  17. Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA Jr, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC: Natural bacterial communities serve as quantitative geochemical biosensors. MBio. 2015, 6:e00326-15. [PMID: 25968645] [PMCID: PMC4436078]

  18. Morshed N, Echols N, Adams PD: Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Acta Cryst. 2015, 71:1147-58 [PMID: 25945580] [PMCID: PMC4427199]

  19. González Fernández-Niño SM, Smith-Moritz AM, Chan LJ, Adams PD, Heazlewood JL, Petzold CJ: Standard flow liquid chromatography for shotgun proteomics in bioenergy research. Front Bioeng Biotechnol. 2015, 3:44. [PMID: 25883932] [PMCID: PMC4381839]

  20. Ebert B, Rautengarten C, Guo X, Xiong G, Stonebloom S, Smith-Moritz AM, Herter T, Chan LJ, Adams PD, Petzold CJ, Pauly M, Willats WG, Heazlewood JL, Scheller HV: Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis. Plant Cell 2015, 27:1218-1227 [PMID: 25804536] [PMCID: PMC4558686]

  21. Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD: FEM: feature-enhanced map. Acta Cryst. 2015, D71:646-666. [PMID: 25760612] [PMCID: PMC4356370]

  22. Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK: Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Acta Cryst. 2015, D71:357-66. [PMID: 25664747] [PMCID: PMC4321489]

  23. Alonso-Gutierrez J, Kim E, Batth TS, Cho N, Hu Q, Chan LJ, Petzold CJ, Hillson NJ, Adams PD, Keasling JD, Garcia-Martin H, Soon Lee T: Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering. Metab Eng. 2015, 28:123-133. [PMID: 25554074] [PMCID: ]

  24. Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC: Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nature Methods 2015, 12:127-130. [PMID: 25532136] [PMCID: PMC4312553]

2014
  1. Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD: Improved crystal orientation and physical properties from single-shot XFEL stills. Acta Cryst. 2014, D70:3299-3309. [PMID: 25478847] [PMCID: PMC4257623]

  2. Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC: Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proc Natl Acad Sci U S A 2014, 111:17887-92. [PMID: 25453071] [PMCID: PMC4273327]

  3. McAndrew R, Pruitt RN, Kamita SG, Pereira JH, Majumdar D, Hammock BD, Adams PD, Ronald PC: Structure of the OsSERK2 leucine-rich repeat extracellular domain. Acta Cryst. 2014, D70:3080-3086. [PMID: 25372696] [PMCID: PMC4220978]

  4. Shih SC, Gach PC, Sustarich J, Simmons BA, Adams PD, Singh S, Singh AK: A droplet-to-digital (D2D) microfluidic device for single cell assays. Lab Chip 2014, 15:225-236. [PMID: 25354549] [PMCID: ]

  5. Urzhumtsev A, Afonine PV, Lunin VY, Terwilliger TC, Adams PD: Metrics for comparison of crystallographic maps. Acta Cryst. 2014, D70:2593-2606. [PMID: 25286844] [PMCID: PMC4188004]

  6. Poust S, Yoon I, Adams PD, Katz L, Petzold CJ, Keasling JD: Understanding the Role of Histidine in the GHSxG Acyltransferase Active Site Motif: Evidence for Histidine Stabilization of the Malonyl-Enzyme Intermediate. PLoS One 2014, 9:e109421. [PMID: 25286165] [PMCID: PMC4186864]

  7. Rhee M, Light YK, Yilmaz S, Adams PD, Saxena D, Meagher RJ, Singh AK: Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. Lab Chip 2014, 14:4533-9. [PMID: 25270338] [PMCID: PMC4213212]

  8. Haushalter RW, Kim W, Chavkin TA, The L, Garber ME, Nhan M, Adams PD, Petzold CJ, Katz L, Keasling JD: Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties. Metab Eng. 2014, 26C:48-56. [PMID: 25250846] [PMCID: ]

  9. Batth TS, Singh P, Ramakrishnan VR, Sousa MM, Chan LJ, Tran HM, Luning EG, Pan EH, Vuu KM, Keasling JD, Adams PD, Petzold CJ: A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins. Metab Eng. 2014, 26:48-56. [PMID: 25205128] [PMCID: ]

  10. McInerney P, Adams P, Hadi MZ: Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase. Molecular Biology International 2014, 287430 [PMID: 25197572] [PMCID: PMC4150459]

  11. Hagen A, Poust S, de Rond T, Yuzawa S, Katz L, Adams PD, Petzold CJ, Keasling JD: In vitro analysis of carboxyacyl substrate tolerance in the loading and first extension modules of Borrelidin PKS. Biochemistry 2014, 53:5975-7. [PMID: 25188840] [PMCID: ]

  12. Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG: A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities. PLoS Comput Biol. 2014, 10:e1003827. [PMID: 25188426] [PMCID: PMC4154649]

  13. Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W: An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nature Commun. 2014, 5:4808. [PMID: 25185801] [PMCID: PMC4155512]

  14. Schmidt M, Perera PN, Weber-Bargioni A, Adams PD, Schuck PJ: Raman Spectroscopic Imaging of Biological Systems. in Imaging Life: Biological Systems from Atoms to Tissues. Eds. Howard GC, Brown WE, Auer M. Oxford University Press. 2014, 339-377.

  15. Rennie EA, Ebert B, Miles GP, Cahoon RE, Christiansen KM, Stonebloom S, Khatab H, Twell D, Petzold CJ, Adams PD, Dupree P, Heazlewood JL, Cahoon EB, Scheller HV: Identification of a Sphingolipid α-Glucuronosyltransferase That Is Essential for Pollen Function in Arabidopsis. Plant Cell. 2014, 26:3314-25. [PMID: 25122154] [PMCID: PMC4371831]

  16. Pereira JH, Petchprayoon C, Hoepker AC, Moriarty N, Fink SJ, Cecere G, Paterson I, Adams PD, Marriott G: Structural and Biochemical Studies of Actin in Complex with Synthetic Macrolide Tail Analogues. ChemMedChem. 2014,9:2286-93. [PMID: 25047814] [PMCID: PMC4213943]

  17. Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK: Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Comm. 2014, 5:4371 [PMID: 25006873] [PMCID: PMC4151126]

  18. Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S: Phylogenomic Guided Identification of Industrially Relevant GH1 β-Glucosidases Through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. ACS Chem. Biol. 2014, 9:2082-2091. [PMID: 24984213] [PMCID: PMC4168791]

  19. Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A: Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance. PLoS One 2014, 9:e101115 [PMID: 24983352] [PMCID: PMC4077768]

  20. Dougherty MJ, Tran HM, Stavila V, Knierim B, George A, Auer M, Adams PD, Hadi MZ: Cellulosic Biomass Pretreatment and Sugar Yields as a Function of Biomass Particle Size. PLoS One 2014, 9:e100836 [PMID: 24971883] [PMCID: PMC4074075]

  21. Kung Y, McAndrew RP, Xie X, Liu CC, Pereira JH, Adams PD, Keasling JD: Constructing Tailored Isoprenoid Products by Structure-Guided Modification of Geranylgeranyl Reductase. Structure 2014, 22:1028-36. [PMID: 24954619] [PMCID: Free article]

  22. Lao J, Oikawa A, Bromley JR, McInerney P, Suttangkakul A, Smith-Moritz AM, Plahar H, Chiu TY, González Fernández-Niño SM, Ebert B, Yang F, Christiansen KM, Hansen SF, Stonebloom S, Adams PD, Ronald PC, Hillson NJ, Hadi MZ, Vega-Sánchez ME, Loqué D, Scheller HV, Heazlewood JL: The Plant Glycosyltransferase Clone Collection for Functional Genomics. Plant J. 2014, 79:517-29. [PMID: 24905498] [PMCID: Free article]

  23. Moriarty NW, Tronrud DE, Adams PD, Karplus PA: Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. FEBS J. 2014, 281:4061-71. [PMID: 24890778] [PMCID: PMC4169323]

  24. Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR: Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS). ACS Chemical Biology. 2014, 9:1470-9. [PMID: 24819174] [PMCID: ]

  25. Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD: Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. Acta Cryst. 2014, D70:1346-1356. [PMID: 24816103] [PMCID: PMC4014122]

  26. Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD: Automated identification of elemental ions in macromolecular crystal structures. Acta Cryst. 2014, D70:1104-1114. [PMID: 24699654] [PMCID: PMC3975891]

  27. Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK: Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods 2014, 11:545-548. [PMID: 24633409] [PMCID: PMC4008696]

  28. George KW, Chen A, Jain A, Batth TS, Baidoo EE, Wang G, Adams PD, Petzold CJ, Keasling JD, Lee TS: Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production. Biotechnol Bioeng. 2014, 111:1648-1658. [PMID: 24615242] [PMCID: ]

  29. Ito J, Herter T, Baidoo EE, Lao J, Vega-Sánchez ME, Michelle Smith-Moritz A, Adams PD, Keasling JD, Usadel B, Petzold CJ, Heazlewood JL: Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry. Anal Biochem. 2014, 448:14-22 [PMID: 24299991] [PMCID: ]

  30. Wall ME, Adams PD, Fraser JS, Sauter NK: Diffuse x-ray scattering to model protein motions. Structure. 2014, 22:182-184. [PMID: 24507780] [PMCID: PMC4070675]

  31. Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD: Automating crystallographic structure solution and refinement of protein-ligand complexes. Acta Cryst. 2014, D70:144-154. [PMID: 24419387] [PMCID: PMC3919266]

  32. Klei HE, Moriarty NW, Echols N, Terwilliger TC, Baldwin ET, Pokross M, Posy S, Adams PD: Ligand placement based on prior structures: the guided ligand-replacement method. Acta Cryst. 2014, D70:134-143. [PMID: 24419386] [PMCID: PMC3919265]

  33. Javidpour P, Pereira JH, Goh EB, McAndrew RP, Ma SM, Friedland GD, Keasling JD, Chhabra SR, Adams PD, Beller HR: Biochemical and Structural Studies of NADH-Dependent FabG Used to Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions. Appl Environ Microbiol. 2014, 80:497-505 [PMID: 24212572] [PMCID: PMC3911115]

2013
  1. Parsons HT, Weinberg CS, Macdonald LJ, Adams PD, Petzold CJ, Strabala TJ, Wagner A, Heazlewood JL: Golgi Enrichment and Proteomic Analysis of Developing Pinus radiata Xylem by Free-Flow Electrophoresis. PLoS One 2013, 8:e84669. [PMID: 24416096] [PMCID: PMC3887118]

  2. Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR: High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production. Front Microbiol. 2013, 4:365 [PMID: 24367356] [PMCID: PMC3854461]

  3. Szmidt-Middleton HL, Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A: Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol. Chem. Eng. Sci. 2013, 103:68-73 [PMID: ] [PMCID: ]

  4. Woo HM, Murray GW, Batth TS, Prasad N, Adams PD, Keasling JD, Petzold CJ, Lee TS: Application of targeted proteomics and biological parts assembly in E. coli to optimize the biosynthesis of an anti-malarial drug precursor, amorpha-4,11-diene. Chem. Eng. Sci. 2013, 103:21-28 [PMID: ] [PMCID: ]

  5. Chen Z, Pereira JH, Liu H, Tran HM, Hsu NS, Dibble D, Singh S, Adams PD, Sapra R, Hadi MZ, Simmons BA, Sale KL: Improved Activity of a Thermophilic Cellulase, Cel5A, from Thermotoga maritima on Ionic Liquid Pretreated Switchgrass. PLoS One 2013, 8:e79725 [PMID: 24244549] [PMCID: PMC3828181]

  6. Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ: Phaser.MRage: automated molecular replacement. Acta Cryst. 2013, D69:2276-2286. [PMID: 24189240] [PMCID: PMC3817702]

  7. Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Hung L-W: Model morphing and sequence assignment after molecular replacement. Acta Cryst. 2013, D69:2244-2250. [PMID: 24189236] [PMCID: PMC3817698]

  8. Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD: Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol. 2013, 31:1039-1046. [PMID: 24142050] [PMCID: ]

  9. Dimaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D: Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods 2013, 10:1102-1104 [PMID: 24076763] [PMCID: PMC4116791]

  10. Nwachukwu JC, Southern MR, Kiefer JR, Afonine PV, Adams PD, Terwilliger TC, Nettles KW: Improved Crystallographic Structures Using Extensive Combinatorial Refinement. Structure 2013, 21:1923-1930. [PMID: 24076406] [PMCID: PMC4070946]

  11. Urzhumtsev A, Afonine PV, Adams PD: TLS from fundamentals to practice. Crystallography Reviews 2013, 19:230-270 [PMID: 25249713] [PMCID: PMC4170067]

  12. Afonine PV, Adams PD: Crystallographic Structure Refinement in a Nutshell. in In Advancing Methods for Biomolecular Crystallography, NATO Science for Peace and Security Series A: Chemistry and Biology. Eds. Read RJ, Urzhumtsev, Lunin VY. Springer Science+Business Media Dordrecht. 2013, 211-219.

  13. Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W: Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proc Natl Acad Sci U S A. 2013, 110:12301-12306. [PMID: 23840063] [PMCID: PMC3725109]

  14. Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams PD, Sale KL, Hadi MZ, Simmons BA, Kent MS, Tullman-Ercek D: Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnol. Biofuels 2013, 6:93. [PMID: 23819686] [PMCID: PMC3716932]

  15. Alonso-Gutierrez J, Chan R, Batth TS, Adams PD, Keasling JD, Petzold CJ, Lee TS: Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production. Metab. Eng. 2013, 19C:33-41 [PMID: 23727191] [PMCID: ]

  16. Chiniquy D, Varanasi P, Oh T, Harholt J, Katnelson J, Singh S, Auer M, Simmons B, Adams PD, Scheller HV, Ronald PC: Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Front. Plant Sci. 2013, 4:83. [PMID: 23596448] [PMCID: PMC3622038]

  17. Singh S, Varanasi P, Singh P, Adams PD, Auer M, Simmons BA: Understanding the impact of ionic liquid pretreatment on cellulose and lignin via thermochemical analysis. Biomass & Bioenergy 2013, 54:276-283. [PMID: ] [PMCID: ]

  18. McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons BA, Adams PD: From soil to structure: a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. J. Biol. Chem. 2013, 288:14985-14992. [PMID: 23580647] [PMCID: PMC3663519]

  19. Chandrasekaran A, Deng K, Koh CY, Takasuka T, Bergeman LF, Fox BG, Adams PD, Singh AK: A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres. Chem. Commun. 2013, 495441-5443. [PMID: 23536035] [PMCID: ]

  20. Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A: Bulk-solvent and overall scaling revisited: faster calculations, improved results. Acta Cryst. 2013, D69:625-634. [PMID: 23519671] [PMCID: PMC3606040]

  21. Chang C, Sustarich J, Bharadwaj R, Chandrasekaran A, Adams PD, Singh AK: Droplet-based microfluidic platform for heterogeneous enzymatic assays. Lab Chip. 2013, 13:1817-1822. [PMID: 23507976] [PMCID: ]

  22. Adams PD, Baker D, Brunger AT, Das R, Dimaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC: Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems. Annu. Rev. Biophys. 2013, 42:265-287. [PMID: 23451892] [PMCID: ]

  23. Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J: Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science 2013, 340:491-495. [PMID: 23413188] [PMCID: PMC3732582]

  24. Varanasi P, Singh P, Auer M, Adams PD, Simmons BA, Singh S: Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnol Biofuels 2013, 6:14. [PMID: 23356589] [PMCID: PMC3579681]

  25. Read RJ, Adams PD, McCoy AJ: Intensity statistics in the presence of translational noncrystallographic symmetry. Acta Cryst. 2013, D69:176-183. [PMID: 23385454] [PMCID: PMC3565438]

2012
  1. Burnley BT, Afonine PV, Adams PD, Gros P: Modelling dynamics in protein crystal structures by ensemble refinement. eLife 2012, 1:e00311. [PMID: 23251785] [PMCID: PMC3524795]

  2. Alonso-Mori R, Kern J, Gildea RJ, Sokaras D, Weng TC, Lassalle-Kaiser B, Tran R, Hattne J, Laksmono H, Hellmich J, Glöckner C, Echols N, Sierra RG, Schafer DW, Sellberg J, Kenney C, Herbst R, Pines J, Hart P, Herrmann S, Grosse-Kunstleve RW, Latimer MJ, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Zouni A, Messinger J, Glatzel P, Sauter NK, Yachandra VK, Yano J, Bergmann U: Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode. Proc. Natl. Acad. Sci. USA 2012, 109:19103-19107. [PMID: 23129631] [PMCID: PMC3511075]

  3. Sierra RG, Laksmono H, Kern J, Tran R, Hattne J, Alonso-Mori R, Lassalle-Kaiser B, Glöckner C, Hellmich J, Schafer DW, Echols N, Gildea RJ, Grosse-Kunstleve RW, Sellberg J, McQueen TA, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Hampton CY, Starodub D, Loh ND, Sokaras D, Weng T-C, Zwart PH, Glatzel P, Milathianaki D, White WE, Adams PD, Williams GJ, Boutet S, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK, Bogan MJ: Nanoflow electrospinning serial femtosecond crystallography. Acta Cryst. 2012, D68:1584-1587 [PMID: 23090408] [PMCID: PMC3478121]

  4. Varanasi P, Singh P, Arora R, Adams PD, Auer M, Simmons BA, Singh S: Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Bioresour. Technol. 2012, 126C:156-161 [PMID: 23073103]

  5. Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling J: Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab. Eng. 2012, 14:653-660. [PMID: 23026122]

  6. Pereira JH, Goh EB, Keasling JD, Beller HR, Adams PD: Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus. Acta Cryst. 2012, D68:1320-1328 [PMID: 22993086] [PMCID: PMC3447401]

  7. McClendon SD, Baath T, Petzold CJ, Adams PD, Simmons BA, Singer SW: Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels. 2012, 5:54 [PMID: 22839529] [PMCID: PMC3507748]

  8. Varanasi P, Katsnelson J, Larson DM, Sharma R, Sharma MK, Vega-Sánchez ME, Zemla M, Loqué D, Ronald PC, Simmons BA, Singh S, Adams PD, Auer M: Mechanical Stress Analysis as a Method to Understand the Impact of Genetically Engineered Rice and Arabidopsis Plants. Industrial Biotechnology 2012, 8:238-244 [PMID: ]

  9. Dougherty MJ, D'haeseleer P, Simmons BA, Adams PD, Hadi MZ: Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization. BMC Biotechnol. 2012, 12:38 [PMID: 22759983] [PMCID: PMC3477009]

  10. Reindl W, Deng K, Cheng X, Singh AK, Simmons BA, Adams PD, Northen TR: Nanostructure-Initiator Mass Spectrometry (NIMS) for the Analysis of Enzyme Activities. Curr. Protoc. Chem. Biol. 2012, 4:123-142 [PMID: ]

  11. Brunger AT, Adams PD: Refinement of X-ray Crystal Structures. In Comprehensive Biophysics, Edward Egelman, Editor-in-Chief., Academic Press, 2012.

  12. Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Grosse-Kunstleve RW, Hung L-W: Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. Acta Cryst. 2012, D68:861-870 [PMID: 22751672] [PMCID: PMC3388814]

  13. McKee AE, Rutherford BJ, Chivian DC, Baidoo EK, Juminaga D, Kuo D, Benke PI, Dietrich JA, Ma SM, Arkin AP, Petzold CJ, Adams PD, Keasling JD, Chhabra SR: Manipulation of the Carbon Storage Regulator System for Metabolite Remodeling and Biofuel Production in Escherichia coli. Microb. Cell Fact. 2012, 11:79 [PMID: 22694848] [PMCID: PMC3460784]

  14. Kern J, Alonso-Mori R, Hellmich J, Tran R, Hattne J, Laksmono H, Glöckner C, Echols N, Sierra RG, Sellberg J, Lassalle-Kaiser B, Gildea RJ, Glatzel P, Grosse-Kunstleve RW, Latimer MJ, McQueen TA, Difiore D, Fry AR, Messerschmidt M, Miahnahri A, Schafer DW, Seibert MM, Sokaras D, Weng TC, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Messinger J, Sauter NK, Zouni A, Bergmann U, Yano J, Yachandra VK: Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proc. Natl. Acad. Sci. U S A 2012, 109:9721-9726 [PMID: 22665786] [PMCID: PMC3382516]

  15. Brunger AT, Adams PD, Frommer P, Fromme R, Levitt M, Schröder GF: Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution. Structure 2012, 20:957-966 [PMID: 22681901] [PMCID: PMC3380535]

  16. Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams PD, Arkin AP, Keasling JD, Blanch HW, Simmons BA, Sale KL, Chivian D, Chhabra SR: Tracing determinants of dual-substrate specificity in glycoside hydrolase family 5. J. Biol. Chem. 2012, 287:25335-25343. [PMID: 22645145] [PMCID: PMC3408205]

  17. Grosse-Kunstleve RW, Terwilliger TC, Sauter NK, Adams PD: Automatic Fortran to C++ conversion with FABLE. Source Code for Biology and Medicine 2012, 7:5 [PMID: 22640868] [PMCID: PMC3448510]

  18. Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD: Graphical tools for macromolecular crystallography in PHENIX. J. Appl. Cryst. 2012, 45:581-586 [PMID: 22675231] [PMCID: PMC3359726]

  19. Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams PD, Petzold CJ: Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics 2012, 12:1289-1299. [PMID: 22577029]

  20. Gifford LK, Carter LG, Gabanyi MJ, Berman HM, Adams PD: The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. J. Struct. Funct. Genomics 2012, 13:57-62. [PMID: 22527514] [PMCID: ]

  21. Greving M, Cheng X, Reindl W, Bowen B, Deng K, Louie K, Nyman M, Cohen J, Singh A, Simmons B, Adams P, Siuzdak G, Northen T:Acoustic deposition with NIMS as a high-throughput enzyme activity assay. Anal. Bioanal. Chem. 2012, 403:707-711. [PMID: 22407334]

  22. Morin A, Urban J, Adams PD, Foster I, Sali A, Baker D, Sliz P: Research priorities. Shining light into black boxes. Science 2012, 336:159-160 [PMID: 22499926]

  23. Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N: phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J. Struct. Funct. Genomics 2012, 13:81-90. [PMID: 22418934] [PMCID: ]

  24. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD: Towards automated crystallographic structure refinement with phenix.refine. Acta Cryst. 2012, D68:352-367 [PMID: 22505256] [PMCID: PMC3322595]

  25. Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD: Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Cryst. 2012, D68:381-390 [PMID: 22505258] [PMCID: PMC3322597]

  26. Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, Levitt M, Schröder GF: Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Cryst. 2012, D68:391-403 [PMID: 22505259] [PMCID: PMC3322598]

  27. Deng K, George KW, Reindl W, Keasling JD, Adams PD, Lee TS, Singh AK, Northen TR: Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme Rapid Commun Mass Spectrom. 2012, 26:611-615 [PMID: 22328213]

  28. Groff D, Benke PI, Batth TS, Bokinsky G, Petzold CJ, Adams PD, Keasling JD: Supplementation of intracellular XylR leads to co-utilization of hemicellulose sugars Appl Environ Microbiol 2012, 78:2221-2229. [PMID: 22286982] [PMCID: PMC3302627]

  29. Perera PN, Schmidt M, Chiang VL, Schuck PJ, Adams PD: Raman-spectroscopy-based noninvasive microanalysis of native lignin structure. Anal. Bioanal. Chem. 2012, 402:983-987. [PMID: 22071606]

2011
  1. Pereira JH, Ralston CY, Douglas NR, Kumar R, Lopez T, McAndrew RP, Knee KM, King JA, Frydman J, Adams PD: Mechanism of nucleotide sensing in group II chaperonins EMBO Journal 2011, 31:731-740 [PMID: 22193720] [PMCID: PMC3273386]

  2. McAndrew RP, Peralta-Yahya PP, DeGiovanni A, Pereira JH, Hadi MZ, Keasling JD, Adams PD: Structure of a Three-Domain Sesquiterpene Synthase: A Prospective Target for Advanced Biofuels Production. Structure 2011, 19:1876-1884 [PMID: 22153510]

  3. Brunger AT, Adams PD, Rice LM: Enhanced Macromolecular Refinement by Simulated Annealing. In International Tables for Crystallography, Volume F: Crystallography of Biological Macromolecules, E. Arnold, D.M Himmel and M.G. Rossmann, Eds., John Wiley and Sons, Ltd., 2011, 466-473.

  4. Brunger AT, Adams PD, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Pannu NS, Read RJ, Rice LM, Simonson T: CNS, a program system for structure-determination and refinement. In International Tables for Crystallography, Volume F: Crystallography of Biological Macromolecules, E. Arnold, D.M Himmel and M.G. Rossmann, Eds., John Wiley and Sons, Ltd., 2011, 512-519.

  5. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH: PHENIX: a comprehensive Python-based system for macromolecular structure solution. In International Tables for Crystallography, Volume F: Crystallography of Biological Macromolecules, E. Arnold, D.M Himmel and M.G. Rossmann, Eds., John Wiley and Sons, Ltd., 2011, 539-547.

  6. Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lutteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH: A New Generation of Crystallographic Validation Tools for the Protein Data Bank. Structure 2011, 19:1395-1412 [PMID: 22000512] [PMCID: PMC3195755]

  7. Gildea RJ, Bourhis LJ, Dolomanov OV, Grosse-Kunstleve RW, Puschmann H, Adams PD, Howard JAK: iotbx.cif: a comprehensive CIF toolbox. J. Appl. Cryst. 2011, 44:1259-1263 [PMID: 22199401] [PMCID: PMC3236671]

  8. Ouellet M, Datta S, Dibble DC, Tamrakar PR, Benke PI, Li C, Singh S, Sale KL, Adams PD, Keasling JD, Simmons BA, Holmes BM, Mukhopadhyay A: Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production. Green Chem. 2011, 13:2743-2749

  9. Reindl W, Deng K, Gladden JM, Cheng G, Wong A, Singer SW, Singh S, Lee JC, Yao CH, Hazen TC, Singh AK, Simmons BA, Adams PD, Northen TR: Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities. Energy & Environmental Science 2011, 4:2884-2893

  10. Perera PN, Schmidt M, Schuck PJ, Adams PD:Blind image analysis for the compositional and structural characterization of plant cell walls. Anal. Chim. Acta. 2011, 702:172-7 [PMID: 21839194]

  11. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH: The Phenix software for automated determination of macromolecular structures. Methods 2011, 55:94-106 [PMID: 21821126] [PMCID: PMC3193589]

  12. Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM: The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J. Struct. Funct. Genomics. 2011, 12:45-54 [PMID: 21472436] [PMCID: PMC3123456]

  13. Grosse-Kunstleve RW, Wong B, Mustyakimov M, Adams PD: Exact direct-space asymmetric units for the 230 crystallographic space groups. Acta Cryst. 2011, A67: [PMID: 21487185] [PMCID: PMC3082335]

  14. Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams PD, Keasling JD, Soon Lee T, Mukhopadhyay A, Petzold CJ: Targeted proteomics for metabolic pathway optimization: Application to terpene production. Metab. Eng. 2011, 13:194-203 [PMID: 21215324]

2010
  1. Achyuthan KE, Achyuthan AM, Adams PD, Dirk SM, Harper JC, Simmons BA, Singh AK: Supramolecular Self-Assembled Chaos: Polyphenolic Lignin's Barrier to Cost-Effective Lignocellulosic Biofuels. Molecules 2010, 15:8641-8688. [PMID: 21116223]

  2. Schmidt M, Perera P, Schwartzberg AM, Adams PD, Schuck PJ: Label-free in situ Imaging of Lignification in Plant Cell Walls. J Vis Exp. 2010, Issue 45. [PMID: 21085100]

  3. Bharadwaj R, Chen Z, Datta S, Holmes BM, Sapra R, Simmons BA, Adams PD, Singh AK: Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion. Anal Chem. 2010, 82:9513-9520. [PMID: 20964411]

  4. Adams P, Langan P: Opportunities and challenges with the growth of neutron crystallography. Acta Cryst. 2010, D66:1121-1123. [PMID: 21041924]

  5. Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD: Joint X-ray and neutron refinement with phenix.refine. Acta Cryst. 2010, D66:1153-1163. [PMID: 21041930] [PMCID: PMC2967420]

  6. Bruning JB, Parent AA, Gil G, Zhao M, Nowak J, Pace MC, Smith CL, Afonine PV, Adams PD, Katzenellenbogen JA, Nettles KW: Coupling of receptor conformation and ligand orientation determine graded activity. Nature Chem. Biol. 2010, 6:837-843. [PMID: 20924370] [PMCID: PMC2974172]

  7. Bharadwaj R, Wong A, Knierim B, Singh S, Holmes BM, Auer M, Simmons BA, Adams PD, Singh AK: High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresource Technol. 2010, 102:1329-1337 [PMID: 20884206]

  8. Chandrasekaran A, Bharadwaj R, Park JI, Sapra R, Adams PD, Singh AK: A Microscale Platform for Integrated Cell-Free Expression and Activity Screening of Cellulases. J. Proteome Res. 2010, 9:5677-5683. [PMID: 20735086]

  9. Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T: Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles. PLoS Computational Biology 2010, 6:e1000911 [PMID: 20865158] [PMCID: PMC2928775]

  10. Tamura L, Ahmed M, Bailey S, Bluhm H, Guo J, Heske C, Hexemer A, Liu Z, MacDowell A, Marcus M, Padmore H, Schoenlein B, Teat S, Tyliszczak, Yang W, Adams P, Falcone R, Hussain Z: Photon Science at the ALS for Sustainable Energy. Synchrotron Radiation News 2010, 23, 4:8-15.

  11. Liu H, Pereira JH, Adams PD, Sapra R, Simmons BA, Sale KL: Molecular Simulations Provide New Insights Into the Role of the Accessory Immunoglobulin-Like Domain of Cel9a. FEBS Lett. 2010, 584:3431-3435. [PMID: 20609364]

  12. Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons BA, Adams PD: Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J. Struct. Biol. 2010, 172:371-379. [PMID: 20599513]

  13. Pereira JH, Ralston CY, Douglas N, Meyer D, Knee KM, Goulet DR, King JA, Frydman J, Adams PD: Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J. Biol. Chem. 2010, 285:27958-27966. [PMID: 20573955] [PMCID: PMC2934662]

  14. Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43:677-685. [PMID: 20648263] [PMCID: PMC2906258]

  15. Schmidt M, Schwartzberg AM, Carroll A, Chaibang A, Adams PD, Schuck PJ: Raman imaging of cell wall polymers in Arabidopsis thaliana. Biochem. and Biophys. Res. Comm. 2010, 395:521-523. [PMID: 20394731]

  16. Achyuthan KE, Adams PD, Datta S, Simmons BA, Singh AK: Hitherto unrecognized fluorescence properties of coniferyl alcohol. Molecules 2010, 15:1645-1667. [PMID: 20336005]

  17. Nishi K, Lee HJ, Park SY, Bae SJ, Lee SE, Adams PD, Rhee JH, Kim JS: Crystal structure of the transcriptional activator HlyU from Vibrio vulnificus CMCP6. FEBS Lett. 2010, 584:1097-1102. [PMID: 20178784]

  18. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. 2010, D66:213-221. [PMID: 20124702] [PMCID: PMC2815670]

2009
  1. Grosse-Kunstleve RW, Terwilliger TC, Adams PD: Experience converting a large Fortran-77 program to C++. Newsletter of the IUCr Commission on Crystallographic Computing 2009, 10:74-83.

  2. Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A: A rapid and inexpensive labeling method for microarray gene expression analysis. BMC Biotechnology 2009, 9:97. [PMID: 19939278] [PMCID: PMC2790446]

  3. Achyuthan KE, Adams PD, Simmons BA, Singh AK: Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products. Molecules 2009, 14:4758-4778. [PMID: 19935474]

  4. Urzhumtsev A, Afonine PV, Adams PD: On the use of logarithmic scales for analysis of diffraction data. Acta Cryst. 2009, D65:1283-1291. [PMID: 19966414] [PMCID: PMC2789003]

  5. Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, Terwilliger TC: Recent developments in phasing and structure refinement for macromolecular crystallography. Current Opinion in Structural Biology 2009, 19:566-572. [PMID: 19700309] [PMCID: PMC2763973]

  6. Moriarty NW, Grosse-Kunstleve RW, Adams PD: electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Cryst. 2009, D65:1074-1080. [PMID: 19770504] [PMCID: PMC2748967]

  7. Praznikar J, Afonine PV, Guncar G, Adams PD, Turk D: Averaged kick maps: less noise, more signal...and probably less bias. Acta Cryst. 2009, D65:921-931. [PMID: 19690370] [PMCID: PMC2733881]

  8. Grosse-Kunstleve RW, Moriarty NW, Adams PD: Torsion Angle Refinement and Dynamics as a tool to aid crystallographic Structure Determination. Proceedings of ASME 2009 International Design Engineering Technical Conferences, San Diego, California 2009, August 30 - September 2. Paper #DETC2009-87737. ASME Press.

  9. Pereira JH, Sapra R, Volponi JV, Kozina CL, Simmons B, Adams PD: Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius. Acta Cryst. 2009, D65:744-750. [PMID: 19622857] [PMCID: PMC2714717]

  10. Afonine PV, Grosse-Kunstleve RW, Urzhumtsev A, Adams PD: Automatic multiple-zone rigid-body refinement with a large convergence radius. J. Appl. Cryst. 2009, 42:607-615. [PMID: 19649324] [PMCID: PMC2712840]

  11. Schmidt M, Schwartzberg AM, Perera PN, Weber-Bargioni A, Carroll A, Sarkar P, Bosneaga E, Urban JJ, Song J, Balakshin MY, Capanema EA, Auer M, Adams PD, Chiang VL, James Schuck P: Label-free in situ imaging of lignification in the cell wall of low lignin transgenic Populus trichocarpa. Planta 2009, 230:589-597. [PMID: 19526248] [PMCID: PMC2715566]

  12. Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung L-W: Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Cryst. 2009, D65:582-601. [PMID: 19465773] [PMCID: PMC2685735]

  13. Adams PD, Mustyakimov M, Afonine PV, Langan P: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. Acta Cryst. 2009, D65:567-573. [PMID: 19465771] [PMCID: PMC2685734]

  14. Urzhumtseva L, Afonine PV, Adams PD, Urzhumtsev A: Crystallographic model quality at a glance. Acta Cryst. 2009, D65:297-300. [PMID: 19237753] [PMCID: PMC2651759]

  15. Berman HM, Westbrook JD, Gabanyi MJ, Tao W, Shah R, Kouranov A, Schwede T, Arnold K, Kiefer F, Bordoli L, Kopp J, Podvinec M, Adams PD, Carter LG, Minor W, Nair R, Baer JL: The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research 2009, 37:D365-D368. [PMID: 19010965] [PMCID: PMC2686438]

2008
  1. Yan J, Adams PD, Angel RJ, Ross NL, Rivers M, Parise JB, Clark SM: The development of an automated data analysis system for high-pressure powder diffraction data collected using an area detector. High Pressure Research 2008, 28:293-298.

  2. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Adams PD, Read RJ, Zwart PH, Hung LW: Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Cryst. 2008, D64:515-524. [PMID: 18453687] [PMCID: PMC2424225]

  3. Langan P, Fisher Z, Kovalevsky A, Mustyakimov M, Sutcliffe Valone A, Unkefer C, Waltman MJ, Coates L, Adams PD, Afonine PV, Bennett B, Dealwis C, Schoenborn BP: Protein structures by spallation neutron crystallography. J. Synchrotron Rad. 2008, 15:215-218. [PMID: 18421142] [PMCID: PMC2394804]

  4. Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD: Automated Structure Solution with the PHENIX Suite. Methods in Molecular Biology 2008, 426:419-435. [PMID: 18542881]

  5. Kim SH, Shin DH, Kim R, Adams P, Chandonia JM: Structural genomics of minimal organisms: pipeline and results. Methods in Molecular Biology 2008, 426:475-496. [PMID: 18542885]

  6. Blanch HW, Adams PD, Andrews-Cramer KM, Frommer WB, Simmons BA, Keasling JD: Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. ACS Chemical Biology 3, 17-20. [PMID: 18205287]

  7. González A, Moorhead P, McPhillips SE, Song J, Sharp K, Taylor JR, Adams PD, Sauter NK, Soltis SM: Web-Ice: integrated data collection and analysis for macromolecular crystallography. J. Appl. Cryst. 2008 41, 176-184.

  8. Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD: Surprises and pitfalls arising from (pseudo)symmetry. Acta Cryst. 2008, D64:99-107. [PMID: 18094473] [PMCID: PMC2394827]

  9. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD: Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Cryst. 2008, D64:61-69. [PMID: 18094468] [PMCID: PMC2394820]

2007
  1. Afonine PV, Grosse-Kunstleve RW, Adams PD, Lunin VY, Urzhumtsev A: On macromolecular refinement at subatomic resolution with interatomic scatterers. Acta Cryst. 2007, D63:1194-1197.

  2. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ: Phaser crystallographic software. J. Appl. Cryst. 2007, 40:658-674.

  3. Bourhis LJ, Grosse-Kunstleve RW, Adams PD: cctbx news Newsletter of the IUCr Commission on Crystallographic Computing 2007, 8:74-80.

  4. Adams PD, Afonine, PV, Grosse-Kunstleve RW, Moriarty NW, Sauter NK, Zwart PH, Gopal K, Ioerger TR, Kanbi L, McKee E, Pai RK, Hung L-W, Radhakannan T, McCoy AJ, Read RJ, Storoni LC, Romo TD, Sacchettini JC, Terwilliger TC: Automated structure determination with Phenix. In Evolving Methods for Macromolecular Crystallography. Read RJ and Sussman JL, Eds., Springer, Dordrecht, The Netherlands. 2007, 101-109.

  5. Morton S, Glossinger J, Smith-Baumann A, McKean JP, Trame C, Dickert J, Rozales A, Dauz A, Taylor J, Zwart P, Duarte R, Padmore H, McDermott G, Adams P: Recent Major Improvements to the ALS Sector 5 Macromolecular Crystallography Beamlines. Synchrotron Radiation News 2007, 20, 4:23-30.

  6. Oganesyan V, Adams PD, Jancarik J, Kim R, Kim SH: Structure of O67745_AQUAE from Aquifex aeolicus resolution. Acta Cryst. 2007, F63:369-374.

  7. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD, Moriarty NW, Zwart P, Read RJ, Turk D, Hung LW: Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Cryst. 2007, D63:597-610.

  8. Terwilliger TC, Adams PD, Moriarty NW, Cohn JD: Ligand identification using electron-density map correlations. Acta Cryst. 2007, D63:101-107.

  9. Hohn M, Tang G, Goodyear G, Baldwin PR, Huang Z, Penczek PA, Yang C, Glaeser RM, Adams PD, Ludtke SJ: SPARX, a new environment for Cryo-EM image processing. J Struct Biol. 2007, 157:47-55.

2006
  1. Zwart PH, Grosse-Kunstleve RW, Adams PD: Exploring Metric Symmetry. CCP4 newsletter, Summer 2006; Contribution 8.

  2. Grosse-Kunstleve RW, Zwart PH, Afonine PV, Ioerger TR, Adams PD: cctbx news Newsletter of the IUCr Commission on Crystallographic Computing 2006, 7:92-105.

  3. Terwilliger TC, Klei H, Adams PD, Moriarty NW, Cohn JD: Automated ligand fitting by core-fragment fitting and extension into density. Acta Cryst. 2006, D62:915-922.

  4. Sauter NK, Grosse-Kunstleve RW, Adams PD: Improved statistics for determining the Patterson symmetry from unmerged diffraction intensities. J. Appl. Cryst. 2006, 39:158-168.

  5. MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA: Structural Basis for Double-Stranded RNA Processing by Dicer. Science 2006, 311:195-198.

2005
  1. Zwart PH, Grosse-Kunstleve RW, Adams PD: Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation. CCP4 newsletter, Winter 2005; Contribution 7.

  2. Xu QS, Jancarik J, Luo Y, Kuznetsova K, Yakunin AF, Yokota H, Adams P, Kim R, Kim SH: Crystal Structures of a phosphotransacetylase from Bacillus subtilis and its complex with acetyl phosphate. J. Struct. Funct. Genomics. 2005, 6:269-279.

  3. Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH: Crystal Structures of an NAD Kinase from Archaeoglobus fulgidus in Complex with ATP, NAD, or NADP. Journal of Molecular Biology 2005, 354:289-303.

  4. McKee EW, Kanbi LD, Childs KL, Grosse-Kunstleve RW, Adams PD, Sacchettini JC, Ioerger TR: FINDMOL: automated identification of macromolecules in electron-density maps Acta Cryst. 2005, D61:1514-1520.

  5. Kim SH, Shin DH, Wang W, Adams PD, Chandonia JM: Overview of Structural Genomics: Landscape, Premises, and Current Direction. In Structural Genomics and High Throughput Structural Biology 2005, M. Sundstrom, M. Norin and A. Edwards, Eds., CRC Press, Taylor and Francis Group.

  6. Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim JS, Das D, Schulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, Degiovanni A, Lou Y, Henriquez M, Huang C, Jancarik J, Pufan R, Choi IG, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams PD, Kim R: Structural genomics of minimal organisms and protein fold space J. Struct Funct Genomics. 2005, 6:63-70.

  7. Aishima J, Russel DS, Guibas LJ, Adams PD, Brunger AT: Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface Acta Cryst. 2005, D61:1354-1363.

  8. Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams PD, Pace NR: Crystal structure of a bacterial ribonuclease P RNA. Proc. Nat. Acad. Sci. USA. 2005, 102:13392-13397.

  9. Afonine PV, Grosse-Kunstleve RW, Adams PD: The Phenix refinement framework. CCP4 newsletter, July 2005; Contribution 8.

  10. Zwart PH, Grosse-Kunstleve RW, Adams PD: Characterisation of X-ray data sets. CCP4 newsletter, July 2005; Contribution 10.

  11. Oganesyan V, Huang C, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH: Structure of a NAD kinase from Thermotoga maritima at 2.3 Å resolution. Acta Cryst. 2005, F61:640-646.

  12. Afonine PV, Grosse-Kunstleve RW, Adams PD: A robust bulk-solvent correction and anisotropic scaling procedure. Acta Cryst. 2005, D61:850-855.

  13. Liu J, Huang C, Shin DH, Yokota H, Jancarik J, Kim JS, Adams PD, Kim R, Kim SH: Crystal Structure of a Heat-inducible Transcriptional Repressor HrcA from Thermotoga maritima: Structural Insight into DNA Binding and Dimerization. Journal of Molecular Biology 2005, 350:987-996.

  14. Oganesyan V, Oganesyan N, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH: Crystal Structure of the "PhoU-Like" Phosphate Uptake Regulator from Aquifex aeolicus. J. Bacteriol. 2005, 187:4238-44.

  15. Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH: A New Class of Metalloprotein Containing Multinuclear Iron Clusters. J. Biol. Chem. 2005, 280:15960-15966.

  16. Grosse-Kunstleve RW, Afonine PV, Sauter NK, Adams PD: cctbx news. IUCr Computing Commission Newsletter 2005, 5:69-91.

  17. Kim JS, DeGiovanni A, Jancarik J, Adams PD, Yokota H, Kim R, Kim SH: Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc. Natl. Acad. Sci. USA. 2005, 102:3248-3253.

2004
  1. Grosse-Kunstleve RW, Afonine PV, Adams PD: cctbx news. IUCr Computing Commission Newsletter 2004, 4:19-36.

  2. Chaudhry C, Horwich AL, Brunger AT, Adams PD: Exploring the structural dynamics of the E. coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. Journal of Molecular Biology 2004, 342:229-245.

  3. Wall JS, Gupta V, Wilkerson M, Schell M, Loris R, Adams P, Solomon A, Stevens F, Dealwis C: Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four Vλ6 proteins J. Mol. Recognition 2004, 17:323-331.

  4. Sauter NK, Grosse-Kunstleve RW, Adams PD: Robust indexing for automatic data collection. J. Appl. Cryst. 2004, 37:399-409.

  5. Grosse-Kunstleve RW, Sauter NK, Adams PD: Numerically stable algorithms for the computation of reduced unit cells. Acta Cryst. 2004, A60:1-6.

  6. Kwon YD, Nagy I, Adams PD, Baumeister W, Jap BK: Crystal Structures of the Rhodococcus Proteasome with and without its Pro-peptides: Implications for the Role of the Pro-peptide in Proteasome Assembly. Journal of Molecular Biology 2004, 335:233-245.

  7. Adams PD, Gopal K, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC: Recent developments in the PHENIX software for automated crystallographic structure determination. J. Synchrotron Rad. 2004, 11:53-55.

  8. Grosse-Kunstleve RW, Sauter NK, Adams PD: cctbx news. IUCr Computing Commission Newsletter 2004, 3:22-31.

  9. Kochva U, Leonov H, Arkin IT, Adams PD: Modeling membrane proteins utilizing information from silent amino acid substitutions. Curr. Protocols in Bioinformatics 2004, Chapter 5, Unit 5.3

2003
  1. Weeks CM, Adams PD, Berendzen J, Brunger AT, Dodson EJ, Grosse-Kunstleve RW, Schneider TR, Sheldrick GM, Terwilliger TC, Turkenburg MG, Uson I: Automatic solution of heavy-atom substructures. Methods Enzymol. 2003, 374:37-83.

  2. Grosse-Kunstleve RW, Adams PD: On symmetries of substructures. Acta Cryst. 2003, D59:1974-1977.

  3. Grosse-Kunstleve RW, Adams PD: Substructure search procedures for macromolecular structures. Acta Cryst. 2003, D59:1966-1973.

  4. Chaudhry C, Farr GW, Todd MJ, Rye HS, Brunger AT, Adams PD, Horwich AL, Sigler PB: Role of the γ-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. EMBO Journal 2003, 22:4877-4887.

  5. Pauly TA, Ekstrom JL, Beebe DA, Chrunyk B, Cunningham D, Griffor M, Kamath A, Lee SE, Madura R, Mcguire D, Subashi T, Wasilko D, Watts P, Mylari BL, Oates PJ, Adams PD, Rath VL: X-Ray Crystallographic and Kinetic Studies of Human Sorbitol Dehydrogenase. Structure 2003, 11:1071-1085.

  6. Grosse-Kunstleve RW, Wong B, Adams PD: cctbx news: Fast triplet generator for direct methods, Gallery of direct-space asymmetric units, et. al. IUCr Computing Commission Newsletter 2003, 2:10-16.

  7. Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR: High-resolution structure of RNase P protein from Thermotoga maritima. Proc. Nat. Acad. Sci. USA. 2003, 100:7497-7502.

  8. Adams PD, Grosse-Kunstleve RW, Brunger AT: Computational aspects of high-throughput crystallographic macromolecular structure determination Methods Biochem. Anal. 2003, 44:75-87.

  9. Grosse-Kunstleve RW, Adams PD: State of the Toolbox: an overview of the Crystallography Toolbox (CCTBX) IUCr Computing Commission Newsletter 2003, 1:28-38.

2002
  1. Adams PD, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC: PHENIX: building new software for automated crystallographic structure determination Acta Cryst. 2002, D58:1948-1954.

  2. Grosse-Kunstleve RW, Adams PD: On the handling of atomic anisotropic displacement parameters J. Appl. Cryst. 2002, 35:477-480.

  3. Gottschalk KE, Adams PD, Brunger AT, Kessler H: Transmembrane signal transduction of the aIIbb3 integrin Protein Science 2002, 11:1800-1812.

  4. Brunger AT, Adams PD: Molecular dynamics applied to X-ray structure refinement Accounts of Chemical Research 2002, 35:404-412.

  5. Grosse-Kunstleve RW, Sauter NK, Moriarty NW, Adams PD: The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework J. Appl. Cryst. 2002, 35:126-136.

  6. Grosse-Kunstleve RW, Adams PD: Algorithms for deriving crystallographic space-group information. II. Treatment of special positions. Acta Cryst. 2002, A58:60-65.

2001
  1. Grosse-Kunstleve RW, Adams PD: Patterson correlation methods: a review of molecular replacement with CNS. Acta Cryst. 2001, D57:1390-1396.

  2. Brunger AT, Adams PD, Rice LM: Enhanced Macromolecular Refinement by Simulated Annealing. In International Tables for Crystallography, Volume F: Macromolecular crystallography, M.G. Rossmann and E. Arnold, Eds., Kluwer Academic Publishers (Dordrecht), 2001, 375-381.

  3. Brunger AT, Adams PD, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Pannu NS, Read RJ, Rice LM, Simonson T: The structure determination language of the Crystallography & NMR System. In International Tables for Crystallography, Volume F: Macromolecular crystallography, M.G. Rossmann and E. Arnold, Eds., Kluwer Academic Publishers (Dordrecht), 2001, 710-716.

2000
  1. Adams PD, Grosse-Kunstleve RW: Recent developments in software for automation of crystallographic macromolecular structure determination. Current Opinion in Structural Biology 2000, 10:564-568.

  2. Torres J, Adams PD, Arkin IT: Use of a new label, 13C=18O, in the determination of a structural model of phospholamban in a lipid bilayer. Spatial restraints resolve the ambiguity arising from the interpretations of mutagenesis data. Journal of Molecular Biology 2000, 300:677-685.

1999
  1. Adams PD, Pannu NS, Read RJ, Brunger AT: Extending the limits of molecular replacement through combined simulated annealing and maximum likelihood refinement. Acta Cryst. 1999, D55:181-190.

  2. Brunger AT, Adams PD, Rice LM: Annealing in crystallography: a powerful optimization tool Progress in Biophysics & Molecular Biology 1999, 72:135-155.

  3. Kukol A, Adams PD, Rice LM, Brunger AT, Arkin IT: Experimentally based orientational refinement of membrane protein models: A structure for the Influenza A M2 H+ channel. Journal of Molecular Biology 1999, 286:951-962.

1998
  1. Brunger AT, Adams PD, Clore GM, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL: Crystallography & NMR system (CNS): A new software system for macromolecular structure determination. Acta Cryst. 1998, D54:905-921.

  2. Brunger AT, Adams PD, Rice LM: Recent developments for the efficient crystallographic refinement of macromolecular structures. Current Opinion in Structural Biology 1998, 8:606-611.

  3. Brunger AT, Adams PD, Rice LM: New Applications of simulated annealing in crystallographic refinement. In Direct Methods for Solving Macromolecular Structures 1998, S. Fortier, Ed., Kluwer, 143-157.

  4. Adams PD, Lee AS, Brunger AT, Engelman DM: Models for the transmembrane region of the phospholamban pentamer: which is correct?. Annals of the New York Academy of Science 1998, 853:178-185.

1997
  1. Adams PD, Pannu NS, Read RJ, Brunger AT: Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Nat. Acad. Sci. USA. 1997, 94:5018-5023.

  2. Brunger AT, Adams PD, Rice LM: New applications of simulated annealing in X-ray crystallography and solution NMR. Structure 1997, 5:325-336.

  3. Arkin IT, Adams PD, Brunger AT, Aimoto S, Engelman DM, Smith SO: Structure of the Transmembrane Cysteine Residues in Phospholamban. J. Membrane Biol. 1997, 155:199-206.

  4. Weissman JS, Fenton WA, Braig K, Adams PD, Horwich AL: Eschericia Coli GroEL, structure and function. In Guidebook to Molecular Chaperones and Protein Folding Sequences 1997, M.-J. Gething, Ed., Oxford University Press, 173-176.

  5. Arkin IT, Adams PD, Brunger AT, Smith SO, Engelman DM: Structural perspectives of phospholamban, a helical transmembrane pentamer. Annual Reviews of Biophysics and Biomolecular Structure 1997, 26:157-222.

  6. Adams PD, Brunger AT: Towards Prediction of Membrane Protein Structure. In Membrane Protein Assembly 1997, G.V. Heijne, Ed., R.G. Landes Co., Austin, TX.

1996
  1. Adams PD, Braig K, Rice LM, Brunger AT: Torsion angle dynamics refinement of the Chaperonin GroEL at 2.8 Å resolution. In Macromolecular refinement, Proceedings of the CCP4 study weekend at Chester College 1996, January 5-6, S. Bailey and E. Dodson, Eds., Council of the Central Laboratory of the Research Councils.

  2. Adams PD, Engelman DM, Brunger AT: An improved prediction for the structure of the dimeric transmembrane domain of Glycophorin A obtained through global searching. Proteins 1996, 26: 257-261.

1995
  1. Braig K, Adams PD, Brunger AT: Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution. Nature Structural Biology 1995, 2:1083-1094.

  2. Adams PD, Arkin IT, Engelman DM, Brunger AT: Computational searching and mutagenesis suggest a structure for phospholamban, a cardiac ion channel. Nature Structural Biology 1995, 2:154-162.

1994
  1. Arkin IT, Adams PD, MacKenzie KR, Lemmon MA, Brunger AT, Engelman DM: Structural organization of the pentameric transmembrane alpha-helices of phospholambin, a cardiac ion channel. EMBO Journal 1994, 13:4757-4764.

  2. Lemmon MA, Treutlein HR, Adams PD, Brunger AT, Engelman DM: A dimerization motif for transmembrane alpha-helices. Nature Structural Biology 1994, 1:157-163.