Paul Adams Publications

2014
  1. 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, epub ahead of print [PMID: ] [PMCID: ]
  2. 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, epub ahead of print [PMID: 24633409] [PMCID: ]
  3. 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, epub ahead of print [PMID: 24615242] [PMCID: ]
  4. 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: ]
  5. Wall ME, Adams PD, Fraser JS, Sauter NK: Diffuse x-ray scattering to model protein motions. Structure. 2014, 22:182-184. [PMID: 24507780] [PMCID: ]
  6. 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: ]
  7. 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: ]
  8. 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: ]
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: ]
  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: PMC3725109]
  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: ]
  11. Urzhumtsev A, Afonine PV, Adams PD: TLS from fundamentals to practice. Crystallography Reviews 2013, 19:230-270 [PMID: ] [PMCID: ]
  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: ]
  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: ]
  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: ]
  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, Loque 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.