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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[pdf]
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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).
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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).
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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)
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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)
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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)
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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)
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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)
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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)
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SOLVE and RESOLVE: automated structure solution and density modification.
T.C. Terwilliger.
Methods Enzymol. 374, 22-36 (2003)
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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)
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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)
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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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[pdf]
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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)
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