Journal Articles

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. 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 J. Struct. Funct. Genomics 12:45-54 (2011)
Copyright © The Authors.
Exact direct-space asymmetric units for the 230 crystallographic space groups. Grosse-Kunstleve RW, Wong B, Mustyakimov M, Adams PD Acta Cryst. A:269-275 (2011)
Copyright © International Union of Crystallography
Joint X-ray and neutron refinement with phenix.refine. Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD. Acta Cryst. D66:1153-1163 (2010)
Copyright © International Union of Crystallography
Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles. Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. PLoS Computational Biology 2010, 6:e1000911 (2010)
Copyright © Public Library of Science Computational Biology
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43:677-685 (2010)
Copyright © International Union of Crystallography
PHENIX: a comprehensive Python-based system for macromolecular structure solution. 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. Acta Cryst. 2010, D66:213-221 (2010)
Copyright © International Union of Crystallography
Autoindexing with outlier rejection and identification of superimposed lattices. N.K. Sauter and B.K. Poon. J. Appl. Cryst. 43, 611-616 (2010)
Copyright © International Union of Crystallography
Detection and correction of underassigned rotational symmetry prior to structure deposition. B.K. Poon, R.W. Grosse-Kunstleve, P.H. Zwart and N.K. Sauter. Acta Cryst. D66, 503-513 (2010)
Copyright © International Union of Crystallography
Autoindexing the diffraction patterns from crystals with a pseudotranslation. N.K. Sauter and P.H. Zwart. Acta Cryst. D65, 553-559 (2009)
Copyright © International Union of Crystallography
On the use of logarithmic scales for analysis of diffraction data. Urzhumtsev A, Afonine PV, Adams PD Acta Cryst. 2009, D65:1283-1291 (2009)
Copyright © International Union of Crystallography
Recent developments in phasing and structure refinement for macromolecular crystallography. Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, Terwilliger TC. Current Opinion in Structural Biology 19:566-572 (2009)
Copyright © Elsevier Ltd.
electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Moriarty NW, Grosse-Kunstleve RW, Adams PD. Acta Cryst. 2009, D65:1074-1080 (2009)
Copyright © International Union of Crystallography
Averaged kick maps: less noise, more signal...and probably less bias. Praznikar J, Afonine PV, Guncar G, Adams PD, Turk D Acta Cryst. 2009, D65:921-931 (2009)
Copyright © International Union of Crystallography
Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius. Pereira JH, Sapra R, Volponi JV, Kozina CL, Simmons B, Adams PD Acta Cryst. 2009, D65:744-750 (2009)
Copyright © International Union of Crystallography
Automatic multiple-zone rigid-body refinement with a large convergence radius. Afonine PV, Grosse-Kunstleve RW, Urzhumtsev A, Adams PD J. Appl. Cryst. 2009, 42:607-615 (2009)
Copyright © International Union of Crystallography
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung L-W Acta Cryst. 2009, D65:582-601 (2009)
Copyright © International Union of Crystallography
Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. Adams PD, Mustyakimov M, Afonine PV, Langan P Acta Cryst. 2009, D65:567-573 (2009)
Copyright © International Union of Crystallography
Crystallographic model quality at a glance. Urzhumtseva L, Afonine PV, Adams PD, Urzhumtsev A Acta Cryst. 2009, D65:297-300 (2009)
Copyright © International Union of Crystallography
The protein structure initiative structural genomics knowledgebase. 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 Nucleic Acids Research 2009, 37:D365-D368 (2009)
Copyright © The Authors
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Adams PD, Read RJ, Zwart PH, Hung LW Acta Cryst. 2008, D64:515-524 (2008)
Copyright © International Union of Crystallography
Protein structures by spallation neutron crystallography. 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 J. Synchrotron Rad. 2008, 15:215-218 (2008)
Copyright © International Union of Crystallography
Web-Ice: integrated data collection and analysis for macromolecular crystallography. A. González, P. Moorhead, S.E. McPhillips, J. Song, K. Sharp, J.R. Taylor, P.D. Adams, N.K. Sauter and S.M. Soltis. J. Appl. Cryst. 41, 176-184 (2008)
Copyright © International Union of Crystallography
Surprises and pitfalls arising from (pseudo)symmetry. P.H. Zwart, R.W. Grosse-Kunstleve, A.A. Lebedev, G.N. Murshudov and P.D. Adams. Acta Cryst. D64, 99-107 (2008)
Copyright © International Union of Crystallography
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, N.W. Moriarty, P.H. Zwart, L.-W. Hung, R.J. Read, and P.D. Adams. Acta Cryst. D64, 61-69 (2008)
Copyright © International Union of Crystallography
On macromolecular refinement at subatomic resolution with interatomic scatterers. Afonine PV, Grosse-Kunstleve RW, Adams PD, Lunin VY, Urzhumtsev A Acta Cryst. D63:1194-1197 (2007)
Copyright © International Union of Crystallography
Phaser crystallographic software. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ J. Appl. Cryst. 40:658-674 (2007)
Copyright © International Union of Crystallography
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD, Moriarty NW, Zwart P, Read RJ, Turk D, Hung LW Acta Cryst. D63:597-610 (2007)
Copyright © International Union of Crystallography
Ligand identification using electron-density map correlations. Terwilliger TC, Adams PD, Moriarty NW, Cohn J Acta Cryst. D63:101-107 (2007)
Copyright © International Union of Crystallography
Automated ligand fitting by core-fragment fitting and extension into density. Terwilliger TC, Klei H, Adams PD, Moriarty NW, Cohn JD Acta Cryst. D62:915-922 (2006)
Copyright © International Union of Crystallography
Improved statistics for determining the Patterson symmetry from unmerged diffraction intensities. N.K. Sauter, R.W. Grosse-Kunstleve, and P.D. Adams. J. Appl. Cryst. 39, 158-168 (2006)
Copyright © International Union of Crystallography
Automated diffraction image analysis and spot searching for high-throughput crystal screening. Z. Zhang, N.K. Sauter, H. van den Bedem, G. Snell and A.M. Deacon. J. Appl. Cryst. 39, 112-119 (2006)
Copyright © International Union of Crystallography
Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface. Aishima J, Russel DS, Guibas LJ, Adams PD, Brunger AT Acta Cryst. D61:1354-1363 (2005)
Copyright © International Union of Crystallography
Crystal structure of a bacterial ribonuclease P RNA. Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams PD, Pace NR Proc. Nat. Acad. Sci. USA. 102:13392-13397 (2005)
Copyright © International Union of Crystallography
A robust bulk-solvent correction and anisotropic scaling procedure. P.V. Afonine, R.W. Grosse-Kunstleve, and P.D. Adams. Acta Cryst. D61, 850-855 (2005)
Copyright © International Union of Crystallography
Crystal Structure of the "PhoU-Like" Phosphate Uptake Regulator from Aquifex aeolicus. Oganesyan V, Oganesyan N, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH J. Bacteriol. 187:4238-44 (2005)
Copyright © American Society for Microbiology
A New Class of Metalloprotein Containing Multinuclear Iron Clusters. Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH J. Biol. Chem. 280:15960-15966 (2005)
Copyright © American Society for Biochemistry and Molecular Biology
Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Kim JS, DeGiovanni A, Jancarik J, Adams PD, Yokota H, Kim R, Kim SH I>Proc. Natl. Acad. Sci. USA. 102:3248-3253 (2005)
Copyright © The National Academy of Sciences
Robust indexing for automatic data collection. N.K. Sauter, R.W. Grosse-Kunstleve, and P.D. Adams. J. Appl. Cryst. 37, 399-409 (2004)
Copyright © International Union of Crystallography
Numerically stable algorithms for the computation of reduced unit cells. R.W. Grosse-Kunstleve, N.K. Sauter and P.D. Adams. Acta Cryst. A60, 1-6 (2004)
Copyright © International Union of Crystallography
Recent developments in the PHENIX software for automated crystallographic structure determination P.D. Adams, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo, J.C. Sacchettini, N.K. Sauter, L.C. Storoni and T.C. Terwilliger. J. Synchrotron Rad. 11, 53-55 (2004)
Copyright © International Union of Crystallography
On symmetries of substructures R.W. Grosse-Kunstleve and P.D. Adams. Acta Cryst. D59, 1974-1977 (2003)
Copyright © International Union of Crystallography
Substructure search procedures for macromolecular structures R.W. Grosse-Kunstleve and P.D. Adams. Acta Cryst. D59, 1966-1973 (2003)
Copyright © International Union of Crystallography
Role of the γ-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. Chaudhry C, Farr GW, Todd MJ, Rye HS, Brunger AT, Adams PD, Horwich AL, Sigler PB EMBO Journal 22:4877-4887 (2003)
Copyright © European Molecular Biology Organization
X-Ray Crystallographic and Kinetic Studies of Human Sorbitol Dehydrogenase. 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 Structure 11:1071-1085 (2003)
Copyright © Cell Press
High-resolution structure of RNase P protein from Thermotoga maritima A.V. Kazantsev, A.A. Krivenko, D.J. Harrington, R.J. Carter, S.R. Holbrook, P.D. Adams, and N.R. Pace. Proc. Natl. Acad. Sci. USA 100, 7497-7502 (2003)
Copyright © The National Academy of Sciences of the USA
PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002)
Copyright © International Union of Crystallography
On the handling of atomic anisotropic displacement parameters R.W. Grosse-Kunstleve and P.D. Adams. J. Appl. Cryst. 35, 477-480 (2002)
Copyright © International Union of Crystallography
Transmembrane signal transduction of the aIIbb3 integrin. Gottschalk KE, Adams PD, Brunger AT, Kessler H Protein Science 11:1800-1812 (2002)
Copyright © The Protein Society
The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. R.W. Grosse-Kunstleve, N.K. Sauter, N.W. Moriarty and P.D. Adams. J. Appl. Cryst. 35, 126-136 (2002)
Copyright © International Union of Crystallography
Algorithms for deriving crystallographic space-group information. II. Treatment of special positions. R.W. Grosse-Kunstleve and P.D. Adams. Acta Cryst. A58, 60-65 (2002)
Copyright © International Union of Crystallography
Patterson correlation methods: a review of molecular replacement with CNS. R.W. Grosse-Kunstleve and P.D. Adams. Acta Cryst. D57, 1390-1396 (2001)
Copyright © International Union of Crystallography
A Highly Automated Heavy-Atom Search Procedure for Macromolecular Structures R. W. Grosse-Kunstleve, and A. T. Brunger. Acta Cryst. D55, 1568-1577 (1999)
Copyright © International Union of Crystallography
Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement P. D. Adams, N. S. Pannu, R. J. Read and A. T. Brunger. Acta Cryst. D55, 181-190 (1999)
Copyright © International Union of Crystallography
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination A. T. Brunger, P. D. Adams, G. M. Clore, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J.-S. Jiang, J. Kuszewski, M. Nilges, N. S. Pannu, R. J. Read, L. M. Rice, T. Simonson and G. L. Warren. Acta Cryst. D54, 905-921 (1998)
Copyright © International Union of Crystallography
Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement P. D. Adams, N. S. Pannu, R. J. Read and A. T. Brunger. Proc. Natl. Acad. Sci. USA 94, 5018-5023 (1997)
Copyright © The National Academy of Sciences of the USA

Newsletters

Experience converting a large Fortran-77 program to C++. R.W. Grosse-Kunstleve, T.C. Terwilliger and P.D. Adams. IUCr Computing Commission Newsletter 10 (2009)
cctbx news. L.J. Bourhis, R.W. Grosse-Kunstleve and P.D. Adams. IUCr Computing Commission Newsletter 8 (2007)
cctbx news. R.W. Grosse-Kunstleve, P.H. Zwart, P.V. Afonine, T.R. Ioerger and P.D. Adams. IUCr Computing Commission Newsletter 7 (2006)
cctbx news. R.W. Grosse-Kunstleve, P.V. Afonine, N.K. Sauter and P.D. Adams. IUCr Computing Commission Newsletter 5 (2005)
cctbx news. R.W. Grosse-Kunstleve, P.V. Afonine and P.D. Adams. IUCr Computing Commission Newsletter 4 (2004)
cctbx news. R.W. Grosse-Kunstleve, N.K. Sauter and P.D. Adams. IUCr Computing Commission Newsletter 3 (2004)
cctbx news: Fast triplet generator for direct methods, Gallery of direct-space asymmetric units, et. al. R.W. Grosse-Kunstleve and P.D. Adams. IUCr Computing Commission Newsletter 2 (2003)
State of the Toolbox: an overview of the Crystallography Toolbox (CCTBX) R.W. Grosse-Kunstleve and P.D. Adams. IUCr Computing Commission Newsletter 1 (2003)