PDB_REDO: constructive validation, more than just looking for errors

The decision-making algorithms and software used in PDB_REDO to re-refine and rebuild crystallographic protein structures in the PDB are presented and discussed.

[1]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[2]  A. Brunger.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[3]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[4]  Gert Vriend,et al.  Increasing the precision of comparative models with YASARA NOVA—a self‐parameterizing force field , 2002, Proteins.

[5]  D S Moss,et al.  Rfree and the rfree ratio. II. Calculation Of the expected values and variances of cross-validation statistics in macromolecular least-squares refinement. , 2000, Acta crystallographica. Section D, Biological crystallography.

[6]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[7]  Ping-Chiang Lyu,et al.  Structural Basis for the Improved Potency of Peroxisome Proliferator‐Activated Receptor (PPAR) Agonists , 2010, ChemMedChem.

[8]  K. N. Trueblood,et al.  On the rigid-body motion of molecules in crystals , 1968 .

[9]  S J Wodak,et al.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. , 1999, Acta crystallographica. Section D, Biological crystallography.

[10]  Brian R Crane,et al.  Electron transfer between cytochrome c and cytochome c peroxidase in single crystals. , 2004, Journal of the American Chemical Society.

[11]  Anastassis Perrakis,et al.  Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank , 2011, Bioinform..

[12]  Dan S. Tawfik,et al.  Antibody Multispecificity Mediated by Conformational Diversity , 2003, Science.

[13]  C. Sander,et al.  Errors in protein structures , 1996, Nature.

[14]  Gert Vriend,et al.  PDB Improvement Starts with Data Deposition , 2007, Science.

[15]  S. French,et al.  On the treatment of negative intensity observations , 1978 .

[16]  Airlie J. McCoy,et al.  β-Edge Interactions in a Pentadecameric Human Antibody Vκ Domain , 2007 .

[17]  Ralf Jauch,et al.  Crystal structures of the Mnk2 kinase domain reveal an inhibitory conformation and a zinc binding site. , 2005, Structure.

[18]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[19]  W. C. Hamilton.  Significance tests on the crystallographic R factor , 1965 .

[20]  R. Diamond.  A real-space refinement procedure for proteins , 1971 .

[21]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[22]  B. Dick,et al.  Characterization of Novel StAR (Steroidogenic Acute Regulatory Protein) Mutations Causing Non-Classic Lipoid Adrenal Hyperplasia , 2011, PloS one.

[23]  Paul D. Adams,et al.  phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics , 2010, Journal of applied crystallography.

[24]  Pradeep Kota,et al.  Gaia: automated quality assessment of protein structure models , 2011, Bioinform..

[25]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[26]  Vincent Breton,et al.  PDB_REDO: automated re-refinement of X-ray structure models in the PDB , 2009, Journal of applied crystallography.

[27]  Haruki Nakamura,et al.  Remediation of the protein data bank archive , 2007, Nucleic Acids Res..

[28]  Jaime Prilusky,et al.  Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules. , 2011, Journal of structural biology.

[29]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[30]  T. A. Jones,et al.  The Uppsala Electron-Density Server. , 2004, Acta crystallographica. Section D, Biological crystallography.

[31]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.

[32]  Jay Painter,et al.  Electronic Reprint Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion , 2005 .

[33]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[34]  Claus-Wilhelm von der Lieth,et al.  pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files , 2004, BMC Bioinformatics.

[35]  Hanka Venselaar,et al.  Functional Analysis of the Kv1.1 N255D Mutation Associated with Autosomal Dominant Hypomagnesemia* , 2009, The Journal of Biological Chemistry.

[36]  David C. Richardson,et al.  MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes , 2004, Nucleic Acids Res..

[37]  Gaetano T. Montelione,et al.  Structural basis for the sequence-specific recognition of human ISG15 by the NS1 protein of influenza B virus , 2011, Proceedings of the National Academy of Sciences.

[38]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[39]  G N Murshudov,et al.  Use of TLS parameters to model anisotropic displacements in macromolecular refinement. , 2001, Acta crystallographica. Section D, Biological crystallography.

[40]  Jaime Prilusky,et al.  Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules , 2008, Genome Biology.

[41]  Gert Vriend,et al.  Everyday , 2020, Oxford Research Encyclopedia of Literature.

[42]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[43]  M Nayal,et al.  Valence screening of water in protein crystals reveals potential Na+ binding sites. , 1996, Journal of molecular biology.

[44]  P Ann Boriack-Sjodin,et al.  Artemin crystal structure reveals insights into heparan sulfate binding. , 2006, Biochemistry.

[45]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[46]  V S Lamzin,et al.  A self-validation technique for protein structure refinement: the extended Hamilton test. , 1996, Acta crystallographica. Section D, Biological crystallography.

[47]  Gert Vriend,et al.  Re-refinement from deposited X-ray data can deliver improved models for most PDB entries , 2009, Acta crystallographica. Section D, Biological crystallography.

[48]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[49]  T. A. Jones,et al.  A graphics model building and refinement system for macromolecules , 1978 .

[50]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[51]  G J Kleywegt,et al.  Efficient rebuilding of protein structures. , 1996, Acta crystallographica. Section D, Biological crystallography.

[52]  D S Moss,et al.  Rfree and the rfree ratio. I. Derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement. , 1998, Acta crystallographica. Section D, Biological crystallography.

[53]  Fei Long,et al.  REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.

[54]  Randy J. Read,et al.  A New Generation of Crystallographic Validation Tools for the Protein Data Bank , 2011, Structure.

[55]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[56]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[57]  Tadayuki Imanaka,et al.  Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly , 2005, Nucleic acids research.