Literature DB >> 11752306

The Protein Data Bank: unifying the archive.

John Westbrook1, Zukang Feng, Shri Jain, T N Bhat, Narmada Thanki, Veerasamy Ravichandran, Gary L Gilliland, Wolfgang Bluhm, Helge Weissig, Douglas S Greer, Philip E Bourne, Helen M Berman.   

Abstract

The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community. We have now produced a collection of mmCIF data files for the PDB archive (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software.

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Year:  2002        PMID： 11752306      PMCID： PMC99110          DOI： 10.1093/nar/30.1.245

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  8 in total

1.  GenBank.

Authors:  D A Benson; I Karsch-Mizrachi; D J Lipman; J Ostell; B A Rapp; D L Wheeler
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  The PDB data uniformity project.

Authors:  T N Bhat; P Bourne; Z Feng; G Gilliland; S Jain; V Ravichandran; B Schneider; K Schneider; N Thanki; H Weissig; J Westbrook; H M Berman
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

Authors:  A A Vaguine; J Richelle; S J Wodak
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-01-01

5.  Errors in protein structures.

Authors:  R W Hooft; G Vriend; C Sander; E E Abola
Journal:  Nature       Date:  1996-05-23       Impact factor: 49.962

6.  AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.

Authors:  R A Laskowski; J A Rullmannn; M W MacArthur; R Kaptein; J M Thornton
Journal:  J Biomol NMR       Date:  1996-12       Impact factor: 2.835

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

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

8.  The SWISS-PROT protein sequence data bank: current status.

Authors:  A Bairoch; B Boeckmann
Journal:  Nucleic Acids Res       Date:  1994-09       Impact factor: 16.971
  8 in total
  94 in total

1.  MMDB: Entrez's 3D-structure database.

Authors:  Yanli Wang; John B Anderson; Jie Chen; Lewis Y Geer; Siqian He; David I Hurwitz; Cynthia A Liebert; Thomas Madej; Gabriele H Marchler; Aron Marchler-Bauer; Anna R Panchenko; Benjamin A Shoemaker; James S Song; Paul A Thiessen; Roxanne A Yamashita; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  SCOP database in 2002: refinements accommodate structural genomics.

Authors:  Loredana Lo Conte; Steven E Brenner; Tim J P Hubbard; Cyrus Chothia; Alexey G Murzin
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  LIGAND: database of chemical compounds and reactions in biological pathways.

Authors:  Susumu Goto; Yasushi Okuno; Masahiro Hattori; Takaaki Nishioka; Minoru Kanehisa
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

4.  eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.

Authors:  Gregory L Moore; Costas D Maranas
Journal:  Nucleic Acids Res       Date:  2002-06-01       Impact factor: 16.971

5.  Can correct protein models be identified?

Authors:  Björn Wallner; Arne Elofsson
Journal:  Protein Sci       Date:  2003-05       Impact factor: 6.725

6.  The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Authors:  Evelyn Camon; Michele Magrane; Daniel Barrell; David Binns; Wolfgang Fleischmann; Paul Kersey; Nicola Mulder; Tom Oinn; John Maslen; Anthony Cox; Rolf Apweiler
Journal:  Genome Res       Date:  2003-03-12       Impact factor: 9.043

7.  ArchDB: automated protein loop classification as a tool for structural genomics.

Authors:  Jordi Espadaler; Narcis Fernandez-Fuentes; Antonio Hermoso; Enrique Querol; Francesc X Aviles; Michael J E Sternberg; Baldomero Oliva
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  The Database of Interacting Proteins: 2004 update.

Authors:  Lukasz Salwinski; Christopher S Miller; Adam J Smith; Frank K Pettit; James U Bowie; David Eisenberg
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

9.  The distribution and query systems of the RCSB Protein Data Bank.

Authors:  Philip E Bourne; Kenneth J Addess; Wolfgang F Bluhm; Li Chen; Nita Deshpande; Zukang Feng; Ward Fleri; Rachel Green; Jeffrey C Merino-Ott; Wayne Townsend-Merino; Helge Weissig; John Westbrook; Helen M Berman
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

10.  MIPS: analysis and annotation of proteins from whole genomes.

Authors:  H W Mewes; C Amid; R Arnold; D Frishman; U Güldener; G Mannhaupt; M Münsterkötter; P Pagel; N Strack; V Stümpflen; J Warfsmann; A Ruepp
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971
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