2014

• 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.
• 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.

2013

• 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
• Urzhumtsev A, Afonine PV, Adams PD: TLS from fundamentals to practice. Crystallography Reviews 2013, 19:230-270
• Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N: New Python-based methods for data processing. Acta Crystallographica Section D: Biological Crystallography D69, 1274-1282. (Reprint)
• 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.
• 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.
• 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.

2012

• Burnley BT, Afonine PV, Adams PD, Gros P: Modelling dynamics in protein crystal structures by ensemble refinement. eLife 2012, 1:e00311.
• 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
• 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
• 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
• 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

2011

• 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.
• 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
• Grosse-Kunstleve RW, Wong B, Mustyakimov M, Adams PD: Exact direct-space asymmetric units for the 230 crystallographic space groups. Acta Cryst. 2011, A67:

2010

• Sauter NK & Poon BK: Autoindexing with outlier rejection and identification of superimposed lattices. J. Appl. Cryst. 43, 611-616. (Reprint)
• Poon BK, Grosse-Kunstleve RW, Zwart PH & Sauter NK: Detection and correction of underassigned rotational symmetry prior to structure deposition. Acta Cryst. D66, 503-513. (Reprint)
• 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.
• 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.
• 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.

• 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.
• Sauter NK, Zwart PH: Autoindexing the diffraction patterns from crystals with a pseudotranslation. Acta Cryst. 2009, D65:553-559.
• Urzhumtsev A, Afonine PV, Adams PD: On the use of logarithmic scales for analysis of diffraction data. Acta Cryst. 2009, D65:1283-1291.
• 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.
• 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.
• 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.
• 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.

• 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.
• 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. 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.

• 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.
• 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.

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

• 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.
• 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.
• Afonine PV, Grosse-Kunstleve RW, Adams PD: A robust bulk-solvent correction and anisotropic scaling procedure. Acta Cryst. 2005, D61:850-855.
• Grosse-Kunstleve RW, Afonine PV, Sauter NK, Adams PD: cctbx news. IUCr Computing Commission Newsletter 2005, 5:69-91.

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

• 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.
• 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.
• 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.

• 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.
• 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.

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

• 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.