The Protein Data Bank archive as an open data resource

The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.

[1]  Dániel Kozma,et al.  PDBTM: Protein Data Bank of transmembrane proteins after 8 years , 2012, Nucleic Acids Res..

[2]  H. Berg Cold Spring Harbor Symposia on Quantitative Biology.: Vol. LII. Evolution of Catalytic Functions. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1987, ISBN 0-87969-054-2, xix + 955 pp., US $150.00. , 1989 .

[3]  VOLUME LXXXI,et al.  Cold Spring Harbor Symposia on Quantitative Biology , 2005, Protoplasma.

[4]  S. Grossman,et al.  Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DMA-binding domain bound to its DNA target , 1992, Nature.

[5]  Michael G. Lerner,et al.  Binding MOAD (Mother Of All Databases) , 2005, Proteins.

[6]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[7]  Wei Yang,et al.  Crystal structure of the site-specific recombinase γδ resolvase complexed with a 34 by cleavage site , 1995, Cell.

[8]  M G Rossmann,et al.  The crystal structure of insulin. 3. Evidence for a 2-fold axis in rhombohedral zinc insulin. , 1966, Journal of molecular biology.

[9]  J. D. Bernal,et al.  X-Ray Photographs of Crystalline Pepsin , 1934, Nature.

[10]  Thierry Langer,et al.  The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery. , 2008, Journal of medicinal chemistry.

[11]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[12]  W. Lipscomb,et al.  X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[13]  T. Hahn International tables for crystallography , 2002 .

[14]  V. Ramakrishnan,et al.  Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics , 2000, Nature.

[15]  S. R. Hall,et al.  International Tables for Crystallography: Definition and exchange of crystallographic data , 2006 .

[16]  Brian McMahon,et al.  Definition and exchange of crystallographic data , 2005 .

[17]  Ian Sillitoe,et al.  Extending CATH: increasing coverage of the protein structure universe and linking structure with function , 2010, Nucleic Acids Res..

[18]  F. Schluenzen,et al.  Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution , 2000, Cell.

[19]  J L Sussman,et al.  Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. , 1978, Journal of molecular biology.

[20]  R. Huber,et al.  The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors , 1983 .

[21]  H M Berman,et al.  CRYSNET, a crystallographic computing network with interactive graphics display. , 1974, Federation proceedings.

[22]  Janet M. Thornton,et al.  PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids , 2004, Nucleic Acids Res..

[23]  A. Joachimiak,et al.  Crystal structure of trp represser/operator complex at atomic resolution , 1988, Nature.

[24]  M. Perutz,et al.  Structure of Hæmoglobin: A Three-Dimensional Fourier Synthesis at 5.5-Å. Resolution, Obtained by X-Ray Analysis , 1960, Nature.

[25]  Renxiao Wang,et al.  The PDBbind database: methodologies and updates. , 2005, Journal of medicinal chemistry.

[26]  Arnaud Céol,et al.  3did: a catalog of domain-based interactions of known three-dimensional structure , 2013, Nucleic Acids Res..

[27]  H. Berman,et al.  The future of the Protein Data Bank. , 2013, Biopolymers.

[28]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

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

[30]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[31]  N. O. Manning,et al.  The protein data bank , 1999, Genetica.

[32]  R. Stein,et al.  J. D. Bernal: The Sage of Science , 2006 .

[33]  G. Montelione,et al.  Recommendations of the wwPDB NMR Validation Task Force. , 2013, Structure.

[34]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

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

[36]  M Barinaga The missing crystallography data. , 1989, Science.

[37]  Baldomero Oliva,et al.  ArchDB 2014: structural classification of loops in proteins , 2013, Nucleic Acids Res..

[38]  T. Jones,et al.  Between objectivity and subjectivity , 1990, Nature.

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

[40]  J. Kendrew,et al.  A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis , 1958, Nature.

[41]  David S. Wishart,et al.  DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs , 2010, Nucleic Acids Res..

[42]  R. G. Hart,et al.  Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution , 1960, Nature.

[43]  Xin Wen,et al.  BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities , 2006, Nucleic Acids Res..

[44]  M. Baker,et al.  Outcome of the First Electron Microscopy Validation Task Force Meeting , 2012, Structure.

[45]  Ian Sillitoe,et al.  The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies , 2008, Nucleic Acids Res..

[46]  Sameer Velankar,et al.  Implementing an X-ray validation pipeline for the Protein Data Bank , 2012, Acta crystallographica. Section D, Biological crystallography.

[47]  John D. Westbrook,et al.  EMDataBank.org: unified data resource for CryoEM , 2010, Nucleic Acids Res..

[48]  Haruki Nakamura,et al.  BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions , 2008, Journal of biomolecular NMR.

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

[50]  Zukang Feng,et al.  The wwPDB common tool for deposition and annotation , 2011 .

[51]  D. M. Blow,et al.  Structure of crystalline -chymotrypsin. V. The atomic structure of tosyl- -chymotrypsin at 2 A resolution. , 1972, Journal of molecular biology.

[52]  M G Rossmann,et al.  The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure. , 1988, Acta crystallographica. Section A, Foundations of crystallography.

[53]  Akira R. Kinjo,et al.  Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format , 2011, Nucleic Acids Res..

[54]  D. Mercola,et al.  Structure of insulin in 4-zinc insulin , 1976, Nature.

[55]  Alexey G. Murzin,et al.  SCOP2 prototype: a new approach to protein structure mining , 2014, Nucleic Acids Res..

[56]  Steven E. Brenner,et al.  SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures , 2013, Nucleic Acids Res..

[57]  L. J. Harris,et al.  Refined structure of an intact IgG2a monoclonal antibody. , 1997, Biochemistry.

[58]  A. Horwich,et al.  The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex , 1997, Nature.