PHENIX Python-based Hierarchical ENvironment for Integrated Xtallography

List of references related to Phenix

Current primary Phenix citation:

  • PHENIX: a comprehensive Python-based system for macromolecular structure solution. P.D. Adams, P.V. Afonine, G. Bunkoczi, 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).

Other articles

The articles below include both papers produced by members of the Phenix collaboration, and works by external groups relating to methods used in Phenix (and elsewhere).

  • Real-space refinement in PHENIX for cryo-EM and crystallography. P.V. Afonine, B.K. Poon, R.J. Read, O.V. Sobolev, T.C. Terwilliger, A. Urzhumtsev, and P.D. Adams. Acta Cryst. D74, 531-544 (2018).

  • New tools for the analysis and validation of cryo-EM maps and atomic models. P.V. Afonine, B.P. Klaholz, N.W. Moriarty, B.K. Poon, O.V. Sobolev, T.C. Terwilliger, P.D. Adams, and A. Urzhumtsev. Acta Cryst. D74, 814-840 (2018).

  • Automated map sharpening by maximization of detail and connectivity. T.C. Terwilliger, P.V. Afonine, Sobolev, OV, and P.D. Adams. bioRxiv (2018).

  • A fully automatic method yielding initial models from high-resolution electron cryo-microscopy maps. T.C. Terwilliger, P.D. Adams, P.V. Afonine, and O.V. Sobolev. bioRxiv (2018).

  • An editor for the generation and customization of geometry restraints. N.W. Moriarty, E.J. Draizen, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 73, 123-130 (2017).

  • Polder maps: improving OMIT maps by excluding bulk solvent. D. Liebschner, P.V. Afonine, N.W. Moriarty, B.K. Poon, O.V. Sobolev, T.C. Terwilliger, and P.D. Adams. Acta Cryst. D73, 148-157 (2017).

  • FEM: feature-enhanced map. P.V. Afonine, N.W. Moriarty, M. Mustyakimov, O.V. Sobolev, T.C. Terwilliger, D. Turk, A. Urzhumtsev, and P.D. Adams. Acta Cryst. D71, 646-666 (2015).

  • Programming new geometry restraints: parallelity of atomic groups. O.V. Sobolev, P.V. Afonine, P.D. Adams, and A. Urzhumtsev. J. Appl. Cryst. 48, 1130-1141 (2015).

  • Automating crystallographic structure solution and refinement of protein-ligand complexes. N. Echols, N.W. Moriarty, H.E. Klei, P.V. Afonine, G. Bunkóczi, J.J. Headd, A.J. McCoy, R.D. Oeffner, R.J. Read, T.C. Terwilliger, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 70, 144-54 (2014).

  • Ligand placement based on prior structures: the guided ligand-replacement method. H.E. Klei, N.W. Moriarty, N. Echols, T.C. Terwilliger, E.T. Baldwin, M. Pokross, S. Posy, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 70, 134-43 (2014).

  • Automated identification of elemental ions in macromolecular crystal structures. N. Echols, N. Morshed, P.V. Afonine, A.J. McCoy, M.D. Miller, R.J. Read, J.S. Richardson, T.C. Terwilliger, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 70, 1104-14 (2014).

  • Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. J.J. Headd, N. Echols, P.V. Afonine, N.W. Moriarty, R.J. Gildea, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 70, 1346-56 (2014).

  • Model morphing and sequence assignment after molecular replacement. T.C. Terwilliger, R.J. Read, P.D. Adams, A.T. Brunger, P.V. Afonine, and L.W. Hung. Acta Crystallogr D Biol Crystallogr 69, 2244-50 (2013).

  • Improved low-resolution crystallographic refinement with Phenix and Rosetta. F. DiMaio, N. Echols, J.J. Headd, T.C. Terwilliger, P.D. Adams, and D. Baker. Nat Methods 10, 1102-4 (2013).

  • SCEDS: protein fragments for molecular replacement in Phaser. A.J. McCoy, R.A. Nicholls, and T.R. Schneider. Acta Cryst. D69 (2013).

  • Phaser.MRage: automated molecular replacement. G. Bunkóczi, N. Echols, A.J. McCoy, R.D. Oeffner, P.D. Adams, and R.J. Read. Acta Crystallogr D Biol Crystallogr 69, 2276-86 (2013).

  • Bulk-solvent and overall scaling revisited: faster calculations, improved results. P.V. Afonine, R.W. Grosse-Kunstleve, P.D. Adams, and A. Urzhumtsev. Acta Crystallogr D Biol Crystallogr 69, 625-34 (2013).

  • Finding non-crystallographic symmetry in density maps of macromolecular structures. T.C. Terwilliger. J Struct Funct Genomics 14, 91-5 (2013).

  • New tool: phenix.real_space_refine. P.V. Afonine, J.J. Headd, T.C. Terwilliger, and P.D. Adams. Computational Crystallography Newsletter 4, 43-44 (2013).

  • Correcting pervasive errors in RNA crystallography through enumerative structure prediction. F.C. Chou, P. Sripakdeevong, S.M. Dibrov, T. Hermann, and R. Das. Nat Methods 10, 74-6 (2012).

  • phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. T.C. Terwilliger, F. Dimaio, R.J. Read, D. Baker, G. Bunkóczi, P.D. Adams, R.W. Grosse-Kunstleve, P.V. Afonine, and N. Echols. J Struct Funct Genomics 13, 81-90 (2012).

  • Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. T.C. Terwilliger, R.J. Read, P.D. Adams, A.T. Brunger, P.V. Afonine, R.W. Grosse-Kunstleve, and L.W. Hung. Acta Crystallogr D Biol Crystallogr 68, 861-70 (2012).

  • X-ray Anomalous Scattering. E.A. Merritt. http://www.bmsc.washington.edu/scatter (2012).

  • Towards automated crystallographic structure refinement with phenix.refine. P.V. Afonine, R.W. Grosse-Kunstleve, N. Echols, J.J. Headd, N.W. Moriarty, M. Mustyakimov, T.C. Terwilliger, A. Urzhumtsev, P.H. Zwart, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 68, 352-67 (2012).

  • Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. J.J. Headd, N. Echols, P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, N.W. Moriarty, D.C. Richardson, J.S. Richardson, and P.D. Adams. Acta Cryst. D68, 381-390 (2012).

  • Graphical tools for macromolecular crystallography in PHENIX. N. Echols, R.W. Grosse-Kunstleve, P.V. Afonine, G. Bunkóczi, V.B. Chen, J.J. Headd, A.J. McCoy, N.W. Moriarty, R.J. Read, D.C. Richardson, J.S. Richardson, T.C. Terwilliger, and P.D. Adams. J. Appl. Cryst. 45, 581-586 (2012).

  • Linking crystallographic model and data quality. P.A. Karplus, and K. Diederichs. Science 336, 1030-1033 (2012).

  • Modelling dynamics in protein crystal structures by ensemble refinement. B.T. Burnley, P.V. Afonine, P.D. Adams, and P.. Gros. eLife 1 (2012).

  • Improved molecular replacement by density- and energy-guided protein structure optimization. F. DiMaio, T.C. Terwilliger, R.J. Read, A. Wlodawer, G. Oberdorfer, U. Wagner, E. Valkov, A. Alon, D. Fass, H.L. Axelrod, D. Das, S.M. Vorobiev, H. Iwaï, P.R. Pokkuluri, and D. Baker. Nature 473, 540-3 (2011).

  • RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. S.J. Fleishman, A. Leaver-Fay, J.E. Corn, E.M. Strauch, S.D. Khare, N. Koga, J. Ashworth, P. Murphy, F. Richter, G. Lemmon, J. Meiler, and D. Baker. PLoS One 6, e20161 (2011).

  • An introduction to data reduction: space-group determination, scaling and intensity statistics. P.R. Evans. Acta Crystallogr D Biol Crystallogr 67, 282-92 (2011).

  • Improvement of molecular-replacement models with Sculptor. G. Bunkóczi, and R.J. Read. Acta Crystallogr D Biol Crystallogr 67, 303-12 (2011).

  • MolProbity: all-atom structure validation for macromolecular crystallography. V.B. Chen, W.B. Arendall, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson. Acta Cryst. D66, 12-21 (2010).

  • Super-resolution biomolecular crystallography with low-resolution data. G.F. Schröder, M. Levitt, and A.T. Brunger. Nature 464, 1218-22 (2010).

  • Features and development of Coot. P. Emsley, B. Lohkamp, W.G. Scott, and K.. Cowtan. Acta Cryst. D66, 486-501 (2010).

  • Rapid model building of alpha-helices in electron-density maps. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 66, 268-75 (2010).

  • Rapid model building of beta-sheets in electron-density maps. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 66, 276-84 (2010).

  • Rapid chain tracing of polypeptide backbones in electron-density maps. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 66, 285-94 (2010).

  • Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. D.E. Tronrud, D.S. Berkholz, and P.A. Karplus. Acta Crystallogr D Biol Crystallogr 66, 834-42 (2010).

  • Efficient Algorithms for the Problems of Enumerating Cut by Non-decreasing Weights. L.-P. Yeh, B.-F. Wang, and H.-H. Su. Algoritmica 5626, 297-312 (2010).

  • Refinement of protein structures into low-resolution density maps using rosetta. F. DiMaio, M.D. Tyka, M.L. Baker, W. Chiu, and D. Baker. J Mol Biol 392, 181-90 (2009).

  • 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 Crystallogr D Biol Crystallogr 65, 582-601 (2009).

  • 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 Crystallogr D Biol Crystallogr 65, 1074-80 (2009).

  • Averaged kick maps: less noise, more signal... and probably less bias. J. Pražnikar, P.V. Afonine, G. Guncar, P.D. Adams, and D. Turk. Acta Crystallogr D Biol Crystallogr 65, 921-31 (2009).

  • Crystallographic model quality at a glance. L. Urzhumtseva, P.V. Afonine, P.D. Adams, and A. Urzhumtsev. Acta Cryst. D65, 297-300 (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 Crystallogr 42, 607-615 (2009).

  • The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. D.A. Keedy, C.J. Williams, J.J. Headd, W.B. Arendall, V.B. Chen, G.J. Kapral, R.A. Gillespie, J.N. Block, A. Zemla, D.C. Richardson, and J.S. Richardson. Proteins 77 Suppl 9, 29-49 (2009).

  • Conformation dependence of backbone geometry in proteins. D.S. Berkholz, M.V. Shapovalov, R.L. Dunbrack, and P.A. Karplus. Structure 17, 1316-25 (2009).

  • 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).

  • 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).

  • Fast procedure for reconstruction of full-atom protein models from reduced representations. P. Rotkiewicz, and J. Skolnick. J Comput Chem 29, 1460-5 (2008).

  • Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. A.T. Brünger. Nature 355, 472-5 (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 Crystallogr D Biol Crystallogr 64, 99-107 (2008).

  • High-resolution structure prediction and the crystallographic phase problem. B. Qian, S. Raman, R. Das, P. Bradley, A.J. McCoy, R.J. Read, and D. Baker. Nature 450, 259-64 (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).

  • 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 Crystallogr D Biol Crystallogr 63, 1194-7 (2007).

  • 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 Crystallogr 40, 658-674 (2007).

  • 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 Crystallogr D Biol Crystallogr 62, 915-22 (2006).

  • Ligand identification using electron-density map correlations. T.C. Terwilliger, P.D. Adams, N.W. Moriarty, and J.D. Cohn. Acta Crystallogr D Biol Crystallogr 63, 101-7 (2006).

  • The Buccaneer software for automated model building. 1. Tracing protein chains. K. Cowtan. Acta Crystallogr D Biol Crystallogr 62, 1002-11 (2006).

  • Protein homology detection by HMM-HMM comparison. J. Söding. Bioinformatics 21, 951-60 (2005).

  • A robust bulk-solvent correction and anisotropic scaling procedure. P.V. Afonine, R.W. Grosse-Kunstleve, and P.D. Adams. Acta Crystallogr D Biol Crystallogr 61, 850-5 (2005).

  • 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).

  • Likelihood-enhanced fast translation functions. A.J. McCoy, R.W. Grosse-Kunstleve, L.C. Storoni, and R.J. Read. Acta Crystallogr D Biol Crystallogr 61, 458-64 (2005).

  • Using prime-and-switch phasing to reduce model bias in molecular replacement. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 60, 2144-9 (2004).

  • SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure. J.W. Wang, J.R. Chen, Y.X. Gu, C.D. Zheng, F. Jiang, H.F. Fan, T.C. Terwilliger, and Q. Hao. Acta Crystallogr D Biol Crystallogr 60, 1244-53 (2004).

  • Simple algorithm for a maximum-likelihood SAD function. A.J. McCoy, L.C. Storoni, and R.J. Read. Acta Crystallogr D Biol Crystallogr 60, 1220-8 (2004).

  • MUSCLE: multiple sequence alignment with high accuracy and high throughput. R.C. Edgar. Nucleic Acids Res 32, 1792-7 (2004).

  • Liking likelihood. A.J. McCoy. Acta Crystallogr D Biol Crystallogr 60, 2169-83 (2004).

  • Likelihood-enhanced fast rotation functions. L.C. Storoni, A.J. McCoy, and R.J. Read. Acta Crystallogr D Biol Crystallogr 60, 432-8 (2004).

  • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. E. Krissinel, and K. Henrick. Acta Crystallogr D Biol Crystallogr 60, 2256-68 (2004).

  • An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision. Y. Boykov, and V. Kolmogorov. IEEE Transactions on Pattern Analysis and Machine Intelligence 26, 1124-1137 (2004).

  • Automated main-chain model building by template matching and iterative fragment extension. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 59, 38-44 (2003).

  • Automated side-chain model building and sequence assignment by template matching. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 59, 45-9 (2003).

  • Statistical density modification using local pattern matching. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 59, 1688-701 (2003).

  • Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 59, 1174-82 (2003).

  • SOLVE and RESOLVE: automated structure solution, density modification and model building. T. Terwilliger. J Synchrotron Radiat 11, 49-52 (2003).

  • Substructure search procedures for macromolecular structures. R.W. Grosse-Kunstleve, and P.D. Adams. Acta Cryst. D59, 1966-1973. (2003).

  • Structure validation by Calpha geometry: phi,psi and Cbeta deviation. S.C. Lovell, I.W. Davis, W.B. Arendall, P.I. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson. Proteins 50, 437-50 (2003).

  • Rapid automatic NCS identification using heavy-atom substructures. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 58, 2213-5 (2002).

  • 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).

  • 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 Crystallogr D Biol Crystallogr 58, 1948-54 (2002).

  • Statistical density modification with non-crystallographic symmetry. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 58, 2082-6 (2002).

  • Map-likelihood phasing. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 57, 1763-75 (2001).

  • Maximum-likelihood density modification using pattern recognition of structural motifs. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 57, 1755-62 (2001).

  • Global indicators of data quality. M.S. Weiss. J. Appl. Cryst. 34, 130-135 (2001).

  • Geometric nomenclature and classification of RNA base pairs. N.B. Leontis, and E. Westhof. RNA 7, 499-512 (2001).

  • Maximum-likelihood density modification. T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 56, 965-72 (2000).

  • Protein domain decomposition using a graph-theoretic approach. Y. Xu, D. Xu, and H.N. Gabow. Bioinformatics 16, 1091-1104 (2000).

  • Improved R-factors for diffraction data analysis in macromolecular crystallography. K. Diederichs, and P.A. Karplus. Nat Struct Biol 4, 269-75 (1997).

  • A simple min-cut algorithm. M. Stoer, and F. Wagner. Journal of the ACM 44, 585-591 (1997).

  • MAD phasing: Bayesian estimates of F(A). T.C. Terwilliger. Acta Crystallogr D Biol Crystallogr 50, 11-6 (1994).

  • Model bias in macromolecular crystal structures. A. Hodel, S.H. Kim, and A.T. Brunger. Acta Cryst. A48, 851-858 (1992).

  • Crystallographic R factor refinement by molecular dynamics. A.T. Brünger, J. Kuriyan, and M. Karplus. Science 235, 458-60 (1987).

  • Improved Fourier coefficients for maps using phases from partial structures with errors. R.J. Read. Acta Crystallographica 42, 140-149 (1986).

  • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. W. Kabsch, and C. Sander. Biopolymers 22, 2577-637 (1984).

  • Stereochemistry of polypeptide chain configurations. G.N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan. J Mol Biol 7, 95-9 (1963).