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).
- Improvement of cryo-EM maps by density modification. T.C. Terwilliger, S.J. Ludtke, R.J. Read, P.D. Adams, and Afonine. bioRxiv (2019).
- Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). P.D. Adams, P.V. Afonine, K. Baskaran, H.M. Berman, J. Berrisford, G. Bricogne, D.G. Brown, S.K. Burley, M. Chen, Z. Feng, C. Flensburg, A. Gutmanas, J.C. Hoch, Y. Ikegawa, Y. Kengaku, E. Krissinel, G. Kurisu, Y. Liang, D. Liebschner, L. Mak, J.L. Markley, N.W. Moriarty, G.N. Murshudov, M. Noble, E. Peisach, I. Persikova, B.K. Poon, O.V. Sobolev, E.L. Ulrich, S. Velankar, C. Vonrhein, J. Westboork, M. Wojdyr, M. Yokochi, and J.Y. Young. Acta Cryst. D75, 451-454 (2019).
- MolProbity: More and better reference data for improved all-atom structure validation. C.J. Williams, B.J. Hintze, J.J. Headd, N.W. Moriarty, V.B. Chen, S. Jain, S.M. Prisant MG Lewis, L.L. Videau, D.A. Keedy, L.N. Deis, I.I.I. Arendall WB, V. Verma, J.S. Snoeyink, P.D. Adams, S.C. Lovell, J.S. Richardson, and D.C. Richardson. Protein Science 27, 293-315 (2018).
- 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).
- Assessment of detailed conformations suggests strategies for improving cryoEM models: helix at lower resolution, ensembles, pre-refinement fixups, and validation at a multi-residue length scale. J.S. Richardson, C.J. Williams, L.L. Videau, V.B. Chen, and D.C. Richardson. Struct Biol 204, 319-328 (2018).
- 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).
- 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).
- 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).
- 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).
- 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).
- Super-resolution biomolecular crystallography with low-resolution data. G.F. Schröder, M. Levitt, and A.T. Brunger. Nature 464, 1218-22 (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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- Geometric nomenclature and classification of RNA base pairs. N.B. Leontis, and E. Westhof. RNA 7, 499-512 (2001).
- Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. W. Kabsch, and C. Sander. Biopolymers 22, 2577-637 (1984).
- The beta bulge: a common small unit of nonrepetitive protein structure. J.S. Richardson, E.D. Getzoff, and D.C. Richardson. PNAS 75(6), 2574-8 (1978).
- Stereochemistry of polypeptide chain configurations. G.N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan. J Mol Biol 7, 95-9 (1963).