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Here are publications from the PHENIX project: Related publications

Efficient merging of data from multiple samples for determination of anomalous substructure. Akey DL, Terwilliger TC, Smith JL Acta Cryst. D72, 296-302 (2016).
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Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal. Terwilliger TC, Bunkóczi G, Hung L-W, Zwart PH, Smith JL, Akey D, Adams PD Acta Cryst. D72, 359-374 (2016).
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Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing. Terwilliger TC, Bunkóczi G, Hung L-W, Zwart PH, Smith JL, Akey DL, Adams PD Acta Cryst. D72, 346-358 (2016).
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RNA Structure Refinement Using the ERRASER-Phenix Pipeline. Chou FC, Echols N, Terwilliger TC, Das R Methods Mol. Biol. 1320, 269-82 (2016).
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A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. Moriarty NW, Tronrud DE, Adams PD, Karplus PA Acta Cryst. D72, 176-179 (2016).
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Macromolecular crystallographic structure refinement. Afonine PV, Urzhumtsev A, Adams PD in Arbor, Celebrating 100 years of modern crystallography 191, a219 (2015).
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Structure and membrane remodeling activity of ESCRT-III helical polymers. McCullough J, Clippinger AK, Talledge N, Skowyra ML, Saunders MG, Naismith TV, Colf LA, Afonine P, Arthur C, Sundquist WI, Hanson PI, Frost A Science 350, 1548-51 (2015).
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From deep TLS validation to ensembles of atomic models built from elemental motions. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD Acta Cryst. D71, 1668-83 (2015).
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The solvent component of macromolecular crystals. Weichenberger CX, Afonine PV, Kantardjieff K, Rupp B Acta Cryst. D71, 1023-38 (2015).
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Protein Crystallography from the Perspective of Technology Developments. Su XD, Zhang H, Terwilliger TC, Liljas A, Xiao J, Dong Y Crystallogr. Rev. 21, 122-153 (2015).
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Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK Acta Cryst. D71, 357-66 (2015).
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Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS Acta Cryst. D71, 1657-67 (2015).
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EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS Nature Methods 12, 943-6 (2015).
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Programming new geometry restraints: parallelity of atomic groups. Sobolev OV, Afonine PV, Adams PD, Urzhumtsev A J. Appl. Cryst. 48, 1130-1141 (2015).
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Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. 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 Structure 23, 1156-67 (2015).
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X-ray structure determination using low-resolution electron microscopy maps for molecular replacement. Jackson RN, McCoy AJ, Terwilliger TC, Read RJ, Wiedenheft B Nature Protocols 10, 1275-84 (2015).
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Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement. Bunkóczi G, Wallner B Read RJ Structure 23, 397-406 (2015).
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NMR Exchange Format: a unified and open standard for representation of NMR restraint data. 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 Nature Struct. Mol. Biol. 22, 433-4 (2015).
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New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM Nucleic Acids Res. 43, 3420-33 (2015).
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Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Morshed N, Echols N, Adams PD Acta Cryst. D71, 1147-58 (2015).
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New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS Nucleic Acids Res. 42, 12833-46 (2015).
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FEM: feature-enhanced map Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD Acta Cryst. D71, 646-666 (2015).
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Computational Methods for RNA Structure Validation and Improvement. Jain S, Richardson DC, Richardson JS Methods Enzymol. 558, 181-212 (2015).
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Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC Nature Methods 12, 127-130 (2015).
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dxtbx: the diffraction experiment toolbox. Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton AW, Echols N, Evans G, Sauter NK, Winter G J. Appl. Cryst. 47, 1459-1465 (2014).
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Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. 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 Nature Comm. 5, 4371 (2014).
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Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. 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 Nature Methods 11, 545-548 (2014).
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Improved crystal orientation and physical properties from single-shot XFEL stills. Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD Acta Cryst. D70, 3299-3309 (2014).
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Metrics for comparison of crystallographic maps. Urzhumtsev A, Afonine PV, Lunin VY, Terwilliger TC, Adams PD Acta Cryst. D70, 2593-2606 (2014).
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Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. Terwilliger TC, Bricogne G Acta Cryst. D70, 2533-43 (2014).
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Diffuse x-ray scattering to model protein motions. Wall ME, Adams PD, Fraser JS, Sauter NK Structure 22, 182-184 (2014).
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Biophysical highlights from 54 years of macromolecular crystallography. Richardson JS, Richardson DC Biophys. J. 106, 510–525 (2014).
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Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. Deis LN, Pemble CW 4th, Qi Y, Hagarman A, Richardson DC, Richardson JS, Oas TG Structure 22, 1467-77 (2014).
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Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Jackson RN, Golden SM, van Erp PB, Carter J, Westra ER, Brouns SJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B. Science 345, 1473-9 (2014).
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An atomic model of brome mosaic virus using direct electron detection and real-space optimization. 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 Nature Comm. 5, 4808 (2014).
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Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. Moriarty NW, Tronrud DE, Adams PD, Karplus PA FEBS Journal 281, 4061–4071 (2014).
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Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD Acta Cryst. D70, 1346-1356 (2014).
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Automated identification of elemental ions in macromolecular crystal structures. Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD Acta Cryst. D70, 1104-1114 (2014).
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Automating crystallographic structure solution and refinement of protein-ligand complexes. Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD Acta Cryst. D70, 144-154 (2014).
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Ligand placement based on prior structures: the guided ligand-replacement method. Klei HE, Moriarty NW, Echols N, Terwilliger TC, Baldwin ET, Pokross M, Posy S, Adams PD Acta Cryst. D70, 134-143 (2014).
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Improving experimental phases for strong reflections prior to density modification. Uervirojnangkoorn M, Hilgenfeld R, Terwilliger TC, Read RJ Acta Cryst. D69, 2039-49 (2013).
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Phaser.MRage: automated molecular replacement. Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ Acta Cryst. D69, 2276-2286 (2013).
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Improved estimates of coordinate error for molecular replacement. Oeffner RD, Bunkóczi G, McCoy AJ, Read RJ. Acta Cryst. D69, 2209-2215 (2013).
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Model morphing and sequence assignment after molecular replacement. Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Hung L-W Acta Cryst. D69, 2244-2250 (2013).
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Improved low-resolution crystallographic refinement with Phenix and Rosetta. Dimaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Nature Methods 10, 1102-1104 (2013).
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Improved Crystallographic Structures Using Extensive Combinatorial Refinement. Nwachukwu JC, Southern MR, Kiefer JR, Afonine PV, Adams PD, Terwilliger TC, Nettles KW. Structure 21, 1923-1930 (2013).
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TLS from fundamentals to practice. Urzhumtsev A, Afonine PV, Adams PD. Crystallography Reviews 19, 230-270 (2013).
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The Zen of Model Anomalies – Correct Most of Them. Treasure the Meaningful Valid Few. Live Serenely with the Rest! Richardson JS, Richardson DC 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., 1-10 (2013).
Extending the Reach of Molecular Replacement. Read RJ, McCoy AJ, Oeffner RD, Bunkóczi G 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., 113-122 (2013).
Model-Building and Reduction of Model Bias in Electron Density Maps. Terwilliger TC 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., 193-203 (2013).
Crystallographic Structure Refinement in a Nutshell. Afonine PV, Adams PD. 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., 211-219 (2013).
Finding non-crystallographic symmetry in density maps of macromolecular structures. Terwilliger TC. J Struct Funct Genomics. 14, 91-5 (2013).
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Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT. Edayathumangalam R, Wu R, Garcia R, Wang Y, Wang W, Kreinbring CA, Bach A, Liao J, Stone TA, Terwilliger TC, Hoang QQ, Belitsky BR, Petsko GA, Ringe D, Liu D Proc Natl Acad Sci U S A. 110, 17820-5 (2013).
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Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W. Proc Natl Acad Sci U S A. 110, 12301-6 (2013).
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New Python-based methods for data processing. Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N Acta Cryst. D69, 1274-82 (2013).
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Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. 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 Science 340, 491-495 (2013).
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Bulk-solvent and overall scaling revisited: faster calculations, improved results. Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A. Acta Cryst. D69, 625-34 (2013).
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Doing molecular biophysics: finding, naming, and picturing signal within complexity. Richardson JS, Richardson DC. Annual Rev Biophys. 42, 1-28 (2013).
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Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Annual Rev Biophys. 42, 265-87 (2013).
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Intensity statistics in the presence of translational noncrystallographic symmetry. Read RJ, Adams PD, McCoy AJ. Acta Cryst. D69, 176-183 (2013).
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Modelling dynamics in protein crystal structures by ensemble refinement. Burnley BT, Afonine PV, Adams PD, Gros P. eLife. 1, e00311 (2012).
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Refinement of X-ray Crystal Structures. Brunger AT, Adams PD. In Comprehensive Biophysics, Edward Egelman, Editor-in-Chief., Academic Press., (2012).
Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Grosse-Kunstleve RW, Hung L-W. Acta Cryst. D68, 861-870 (2012).
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Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode. 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 Proc. Natl. Acad. Sci. USA 109, 19103-19107 (2012).
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Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution. Brunger AT, Adams PD, Fromme P, Fromme R, Levitt M, Schröder GF. Structure. 20, 957-966 (2012).
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Nanoflow electrospinning serial femtosecond crystallography. 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 Acta Cryst. D68, 1584-1587 (2012).
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Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. 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 Proc. Natl. Acad. Sci. USA 109, 9721-9726 (2012).
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Automatic Fortran to C++ conversion with FABLE. Grosse-Kunstleve RW, Terwilliger TC, Sauter NK, Adams PD. Source Code for Biology and Medicine. 7, 5 (2012).
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Graphical tools for macromolecular crystallography in PHENIX. 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. J. Appl. Cryst. 45, 581-586 (2012).
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Research priorities. Shining light into black boxes. Morin A, Urban J, Adams PD, Foster I, Sali A, Baker D, Sliz P. Science. 336, 159-160 (2012).
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phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N. J. Struct. Funct. Genomics. , (2012).
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Towards automated crystallographic structure refinement with phenix.refine. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD. Acta Cryst. D68, 352-367 (2012).
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Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD. Acta Cryst. D68, 381-390 (2012).
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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. Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, Levitt M, Schröder GF. Acta Cryst. D68, 391-403 (2012).
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Enhanced macromolecular refinement by simulated annealing 10.Brunger AT, Adams PD, Rice LM 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., 466-473 (2012).
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. 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., 539-547 (2012).
KiNG and Kinemages Chen VB, Richardson JS, Richardson DC 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., 688-693 (2012).
MolProbity: all-atom structure validation for macromolecular crystallography. Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson, JS, Richardson DC 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., 694-701 (2012).
A New Generation of Crystallographic Validation Tools for the Protein Data Bank. 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. Structure. 19, 1395-1412 (2011).
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iotbx.cif: a comprehensive CIF toolbox. Gildea RJ, Bourhis LJ, Dolomanov OV, Grosse-Kunstleve RW, Puschmann H, Adams PD, Howard JAK. J. Appl. Cryst. 44, 1259-1263 (2011).
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The Phenix software for automated determination of macromolecular structures. 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. Methods. 55, 94-106 (2011).
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Improved molecular replacement by density- and energy-guided protein structure optimization. DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D. Nature. 473, 540-543 (2011).
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Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH Science. 332, 981-984 (2011).
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Improvement of molecular-replacement models with Sculptor. Bunkóczi G, Read RJ Acta Cryst. D67, 303-312 (2011).
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Using SAD data in Phaser. Read RJ, McCoy AJ Acta Cryst. D67, 338-344 (2011).
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Experimental phasing: best practice and pitfalls. McCoy AJ, Read RJ Acta Cryst. D66, 458-469 (2010).
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Joint X-ray and neutron refinement with phenix.refine. P.V. Afonine, M. Mustyakimov, R.W. Grosse-Kunstleve, N.W. Moriarty, P. Langan and P.D. Adams Acta Cryst. D66, 1153-1163 (2010).
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phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 43, 677-685 (2010).
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On the use of logarithmic scales for analysis of diffraction data. A. Urzhumtsev, P.V. Afonine, and P.D. Adams Acta Cryst. D65, 1283-1291 (2010).
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Rapid chain tracing of polypeptide backbones in electron-density maps. T. C. Terwilliger Acta Cryst. D66, 285-294 (2010).
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Rapid model building of beta-sheets in electron-density maps. T. C. Terwilliger Acta Cryst. D66, 276-284 (2010).
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Rapid model building of alpha-helices in electron-density maps. T. C. Terwilliger Acta Cryst. D66, 268-275 (2010).
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PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart Acta Cryst. D66, 213-221 (2010).
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Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. J. J. Headd, R. M. Immormino, D. A. Keedy, P. Emsley, D. C. Richardson and J. S. Richardson J. Struct. Funct. Genomics 10, 83-93 (2009)
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Experience converting a large Fortran-77 program to C++. R. W. Grosse-Kunstleve, T. C. Terwilliger and P. D. Adams Newsletter of the IUCr Commission on Crystallographic Computing 10, 74-83 (2009).
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electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. N. W. Moriarty, R. W. Grosse-Kunstleve and P. D. Adams Acta Cryst. D65, 1074-1080 (2009).
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Averaged kick maps: less noise, more signal...and probably less bias. J. Praznikar, P. V. Afonine, G. Guncar, P. D. Adams and D. Turk Acta Cryst. D65, 921-931 (2009).
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Recent developments in phasing and structure refinement for macromolecular crystallography. P. D. Adams, P. V. Afonine, R. W. Grosse-Kunstleve, R. J. Read, J. S. Richardson, D. C. Richardson, and T. C. Terwilliger Current Opinion in Structural Biology 19, 566-572 (2009).
Torsion Angle Refinement and Dynamics as a tool to aid crystallographic Structure Determination. R. W. Grosse-Kunstleve, N. W. Moriarty and P. D. Adams Proceedings of ASME 2009 International Design Engineering Technical Conferences, San Diego, California, August 30 - September 2 (2009).
Automatic multiple-zone rigid-body refinement with a large convergence radius. P. V. Afonine, R. W. Grosse-Kunstleve, A. Urzhumtsev and P. D. Adams J. Appl. Cryst. 42, 607-615 (2009)
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Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. T. C. Terwilliger, P. D. Adams, R. J. Read, A. J. McCoy, N. W. Moriarty, R. W. Grosse-Kunstleve, P. V. Afonine, P. H. Zwart and L.-W. Hung Acta Cryst. D65, 582-601 (2009)
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Crystallographic model quality at a glance. L. Urzhumtseva, P. V. Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009)
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Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. D. Adams, R. J. Read, P. H. Zwart and L.-W. Hung Acta Cryst. D64, 515-524 (2008)
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Automated Structure Solution with the PHENIX Suite. P. H. Zwart, P. V. Afonine, R. W. Grosse-Kunstleve, L.-W. Hung, T. R. Ioerger, A. J. McCoy, E. McKee, N. W. Moriarty, R. J. Read, J. C. Sacchettini, N. K. Sauter, L. C. Storoni, T. C. Terwilliger, P. D. Adams Methods in Molecular Biology 426, 419-435 (2008)
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)
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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)
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On macromolecular refinement at subatomic resolution with interatomic scatterers. P. V. Afonine, R. W. Grosse-Kunstleve, P. D. Adams, V. Y. Lunin and A. Urzhumtsev Acta Cryst. D63, 1194-1197 (2007)
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Phaser crystallographic software. A. J. McCoy, R. W. Grosse-Kunstleve, P. D. Adams, M. D. Winn, L. C. Storoni and R. J. Read J. Appl. Cryst. 40, 658-674 (2007)
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Automated structure determination with Phenix. P. D. Adams, P. V. Afonine, R. W. Grosse-Kunstleve, N. W. Moriarty, N. K. Sauter, P. H. Zwart, K. Gopal, T. R. Ioerger, L. Kanbi, E. McKee, R. K. Pai, L.-W. Hung, T. Radhakannan, A. J. McCoy, R. J. Read, L. C. Storoni, T. D. Romo, J. C. Sacchettini, and T. C. Terwilliger. In Evolving Methods for Macromolecular Crystallography, R. J. Read and J. L. Sussman, Eds. Springer, Dorcrecht, The Netherlands, 101-109 (2007)
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, P. D. Adams, N. W. Moriarty, P. H. Zwart, R. J. Read, D. Turk and L.-W. Hung Acta Cryst. D63, 597-610 (2007)
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Ligand identification using electron-density map correlations. T. C. Terwilliger, P. D. Adams, N. W. Moriarty and J. D. Cohn Acta Cryst. D63, 101-107 (2007)
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Crystallographic protein model-building on the web. K. Gopal, E. McKee, T. Romo, R. Pai, J. Smith, J. Sacchettini, and T. Ioerger Bioinformatics 23, 375-377 (2007)
Exploring Metric Symmetry. P.H. Zwart, R.W. Grosse-Kunstleve, and P.D. Adams CCP4 newsletter Summer, Contribution 8 (2006)
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Automated ligand fitting by core-fragment fitting and extension into density. T. C. Terwilliger, H. Klei, P. D. Adams, N. W. Moriarty and J. D. Cohn Acta Cryst. D62, 915-922 (2006)
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Improving amino-acid identification, fit and C-alpha prediction using the Simplex method in automated model building. T. D. Romo, J. C. Sacchettini and T. R. Ioerger Acta Cryst. D62, 1401-1406 (2006)
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Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach. R. Pai, J. Sacchettini and T. Ioerger Acta Cryst. D62, 1012-1021 (2006)
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Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation. P.H. Zwart, R.W. Grosse-Kunstleve, and P.D. Adams CCP4 newsletter Winter, Contribution 7 (2005)
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Likelihood-enhanced fast translation functions. A.J. McCoy, R.W. Grosse-Kunstleve, L.C. Storoni & R.J. Read Acta Cryst. D61, 458-464 (2005)
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FINDMOL: automated identification of macromolecules in electron-density maps. E. W. McKee, L. D. Kanbi, K. L. Childs, R. W. Grosse-Kunstleve, P. D. Adams, J. C. Sacchettini and T. R. Ioerger Acta Cryst. D61, 1514-1520 (2005)
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The Phenix refinement framework. P. V. Afonine, R. W. Grosse-Kunstleve and P. D. Adams CCP4 Newsletter July, Contribution 8 (2005)
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Characterisation of X-ray data sets. P. H. Zwart, R. W. Grosse-Kunstleve and P. D. Adams CCP4 Newsletter July, Contribution 10 (2005)
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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)
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cctbx news. R.W. Grosse-Kunstleve, P.V. Afonine, N.K. Sauter and P.D. Adams. IUCr Computing Commission Newsletter 5 69-91 (2005)
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Automated detection of disulfide bridges in electron density maps using linear discriminant analysis. T. R. Ioerger. J. Appl. Cryst. 38, 121-125 (2005)
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cctbx news. R.W. Grosse-Kunstleve, and P.D. Adams. IUCr Computing Commission Newsletter 4 19-36 (2004)
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Using prime-and-switch phasing to reduce model bias in molecular replacement. T. C. Terwilliger Acta Cryst. D60, 2144-2149 (2004)
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Likelihood-enhanced fast rotation functions. L.C. Storoni, A.J. McCoy and R.J. Read. Acta Cryst. D60, 432-438 (2004)
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Evaluation of Geometric and Probabilistic Distance Measures to Retrieve Electron Density Patterns for Protein Structure Determination. K. Gopal, T.D. Romo, J.C. Sacchettini and T.R. Ioerger. Proceedings of the International Conference on Artificial Intelligence, (2004)
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)
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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)
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SOLVE and RESOLVE: automated structure solution, density modification and model building. T.C. Terwilliger. J. Synchrotron Rad. 11, 49-52 (2004)
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cctbx news. R.W. Grosse-Kunstleve, N.K. Sauter and P.D. Adams. IUCr Computing Commission Newsletter 3 22-31 (2004)
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The TEXTAL System: Artificial Intelligence Techniques for Automated Protein Model Building. T.R. Ioerger and J.C. Sacchettini. Methods Enzymol. 374, 244-270 (2003)
Automatic solution of heavy-atom substructures. C.M. Weeks, P.D. Adams, J. Berendzen, A.T. Brunger, E.J. Dodson, R.W. Grosse-Kunstleve, T.R. Schneider, G.M. Sheldrick, T.C. Terwilliger, M.G. Turkenburg, I. Uson. Methods Enzymol. 374, 37-82 (2003)
SOLVE and RESOLVE: automated structure solution and density modification. T.C. Terwilliger. Methods Enzymol. 374, 22-36 (2003)
New ways of looking at experimental phasing. R.J. Read. Acta Cryst. D59, 1891-1902 (2003)
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On symmetries of substructures. R.W. Grosse-Kunstleve and P.D. Adams. Acta Cryst. D59, 1974-1977 (2003)
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Substructure search procedures for macromolecular structures. R.W. Grosse-Kunstleve and P.D. Adams. Acta Cryst. D59, 1966-1973 (2003)
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TEXTAL: Artificial Intelligence Techniques for Automated Protein Structure Determination. K. Gopal, R. Pai, T.R. Ioerger, T. Romo, and J.C. Sacchettini. Proceedings of the 15th Conference on Innovative Applications of Artificial Intelligence (IAAI), 93-100 (2003)
Statistical density modification using local pattern matching. T.C. Terwilliger. Acta Cryst. D59, 1688-1701 (2003)
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Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement. T.C. Terwilliger. Acta Cryst. D59, 1174-1182 (2003)
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Computational aspects of high-throughput crystallographic macromolecular structure determination. P.D. Adams, R.W. Grosse-Kunstleve and A.T. Brunger. Methods Biochem. Anal. 44, 75-87 (2003)
cctbx news: Fast triplet generator for direct methods, Gallery of direct-space asymmetric units, et. al.. R.W. Grosse-Kunstleve, Buddy Wong and P.D. Adams. IUCr Computing Commission Newsletter 2 (2003)
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Automated side-chain model building and sequence assignment by template matching. T.C. Terwilliger. Acta Cryst. D59, 45-49 (2003)
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Automated main-chain model building by template matching and iterative fragment extension. T.C. Terwilliger. Acta Cryst. D59, 38-44 (2003)
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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)
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Automatic modeling of protein backbones in electron density maps via prediction of C-alpha coordinates. T.R. Ioerger, and J.C. Sacchettini. Acta Cryst. D58, 2043-2054 (2002)
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Rapid automatic NCS identification using heavy-atom substructures T.C. Terwilliger. Acta Cryst. D58, 2213-2215 (2002)
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Statistical density modification with non-crystallographic symmetry T.C. Terwilliger. Acta Cryst. D58, 2082-2086 (2002)
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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)
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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)
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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)
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Recent developments in software for automation of crystallographic macromolecular structure determination. P.D. Adams and R.W. Grosse-Kunstleve. Current Opinion in Structural Biology 10, 564-568 (2000)