Paul Adams publications

2008

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.

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.

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.

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.

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.

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.

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

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.

2007

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.

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

Bourhis LJ, Grosse-Kunstleve RW, Adams PD: cctbx news Newsletter of the IUCr Commission on Crystallographic Computing 2007, 7:74-80.

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.

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.

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

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.

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

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

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

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

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.

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.

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

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

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

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.

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.

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

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

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.

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.

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

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

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.

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

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

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.

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.

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.

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.

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

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

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.

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

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

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

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.

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

2001

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

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.

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

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.

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

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.

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

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

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.

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.

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.

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

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.

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

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.

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.

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.

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

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.

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

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.

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

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.

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