Literature DB >> 24010707

How community has shaped the Protein Data Bank.

Helen M Berman1, Gerard J Kleywegt, Haruki Nakamura, John L Markley.   

Abstract

Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules. Since then, the number, size, and complexity of structural models have continued to grow, reflecting the productivity of structural biology. Managed by the Worldwide PDB organization, the PDB has been able to meet increasing demands for the quantity of structural information and of quality. In addition to providing unrestricted access to structural information, the PDB also works to promote data standards and to raise the profile of structural biology with broader audiences. In this perspective, we describe the history of PDB and the many ways in which the community continues to shape the archive.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 24010707      PMCID: PMC4435976          DOI: 10.1016/j.str.2013.07.010

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  29 in total

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Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

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Authors:  Paul D Adams; Ralf W Grosse-Kunstleve; Li Wei Hung; Thomas R Ioerger; Airlie J McCoy; Nigel W Moriarty; Randy J Read; James C Sacchettini; Nicholas K Sauter; Thomas C Terwilliger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-10-21

3.  Announcing the worldwide Protein Data Bank.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura
Journal:  Nat Struct Biol       Date:  2003-12

4.  A three-dimensional model of the myoglobin molecule obtained by x-ray analysis.

Authors:  J C KENDREW; G BODO; H M DINTZIS; R G PARRISH; H WYCKOFF; D C PHILLIPS
Journal:  Nature       Date:  1958-03-08       Impact factor: 49.962

5.  Outcome of a workshop on archiving structural models of biological macromolecules.

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Journal:  Structure       Date:  2006-08       Impact factor: 5.006

6.  PDBML: the representation of archival macromolecular structure data in XML.

Authors:  John Westbrook; Nobutoshi Ito; Haruki Nakamura; Kim Henrick; Helen M Berman
Journal:  Bioinformatics       Date:  2004-10-27       Impact factor: 6.937

7.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

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Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

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Authors:  M Barinaga
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Authors:  Helen Berman; Kim Henrick; Haruki Nakamura; John L Markley
Journal:  Nucleic Acids Res       Date:  2006-11-16       Impact factor: 16.971

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Journal:  Structure       Date:  2016-01-05       Impact factor: 5.006

Review 3.  The future of crystallography in drug discovery.

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Journal:  Expert Opin Drug Discov       Date:  2013-12-28       Impact factor: 6.098

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7.  Improving virtual screening of G protein-coupled receptors via ligand-directed modeling.

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Authors:  Aleksandras Gutmanas; Younes Alhroub; Gary M Battle; John M Berrisford; Estelle Bochet; Matthew J Conroy; Jose M Dana; Manuel A Fernandez Montecelo; Glen van Ginkel; Swanand P Gore; Pauline Haslam; Rowan Hatherley; Pieter M S Hendrickx; Miriam Hirshberg; Ingvar Lagerstedt; Saqib Mir; Abhik Mukhopadhyay; Thomas J Oldfield; Ardan Patwardhan; Luana Rinaldi; Gaurav Sahni; Eduardo Sanz-García; Sanchayita Sen; Robert A Slowley; Sameer Velankar; Michael E Wainwright; Gerard J Kleywegt
Journal:  Nucleic Acids Res       Date:  2013-11-27       Impact factor: 16.971

Review 10.  Computational methods for analysis and inference of kinase/inhibitor relationships.

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