Literature DB >> 12520059

The Protein Data Bank and structural genomics.

John Westbrook1, Zukang Feng, Li Chen, Huanwang Yang, Helen M Berman.   

Abstract

The Protein Data Bank (PDB; http://www.pdb.org/) continues to be actively involved in various aspects of the informatics of structural genomics projects--developing and maintaining the Target Registration Database (TargetDB), organizing data dictionaries that will define the specification for the exchange and deposition of data with the structural genomics centers and creating software tools to capture data from standard structure determination applications.

Mesh：

Year:  2003        PMID： 12520059      PMCID： PMC165515          DOI： 10.1093/nar/gkg068

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


  7 in total

1.  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

2.  STAR/mmCIF: an ontology for macromolecular structure.

Authors:  J D Westbrook; P E Bourne
Journal:  Bioinformatics       Date:  2000-02       Impact factor: 6.937

3.  The Protein Data Bank and the challenge of structural genomics.

Authors:  H M Berman; T N Bhat; P E Bourne; Z Feng; G Gilliland; H Weissig; J Westbrook
Journal:  Nat Struct Biol       Date:  2000-11

4.  Macromolecular Crystallographic Information File.

Authors:  P E Bourne; H M Berman; B McMahon; K D Watenpaugh; J D Westbrook; P M Fitzgerald
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

5.  The PRESAGE database for structural genomics.

Authors:  S E Brenner; D Barken; M Levitt
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

6.  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

7.  Improved tools for biological sequence comparison.

Authors:  W R Pearson; D J Lipman
Journal:  Proc Natl Acad Sci U S A       Date:  1988-04       Impact factor: 11.205
  7 in total
  116 in total

1.  SPINE 2: a system for collaborative structural proteomics within a federated database framework.

Authors:  Chern-Sing Goh; Ning Lan; Nathaniel Echols; Shawn M Douglas; Duncan Milburn; Paul Bertone; Rong Xiao; Li-Chung Ma; Deyou Zheng; Zeba Wunderlich; Tom Acton; Gaetano T Montelione; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2003-06-01       Impact factor: 16.971

2.  The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.

Authors:  Jürgen Kopp; Torsten Schwede
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  FLAGdb++: a database for the functional analysis of the Arabidopsis genome.

Authors:  Franck Samson; Véronique Brunaud; Sylvain Duchêne; Yannick De Oliveira; Michel Caboche; Alain Lecharny; Sébastien Aubourg
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols.

Authors:  Lee Whitmore; B A Wallace
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  UniProt: the Universal Protein knowledgebase.

Authors:  Rolf Apweiler; Amos Bairoch; Cathy H Wu; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Darren A Natale; Claire O'Donovan; Nicole Redaschi; Lai-Su L Yeh
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  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

7.  AANT: the Amino Acid-Nucleotide Interaction Database.

Authors:  Michael M Hoffman; Maksim A Khrapov; J Colin Cox; Jianchao Yao; Lingnan Tong; Andrew D Ellington
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  The RESID Database of Protein Modifications: 2003 developments.

Authors:  John S Garavelli
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

9.  Motif3D: Relating protein sequence motifs to 3D structure.

Authors:  Anna Gaulton; Teresa K Attwood
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

10.  dictyBase: a new Dictyostelium discoideum genome database.

Authors:  Lisa Kreppel; Petra Fey; Pascale Gaudet; Eric Just; Warren A Kibbe; Rex L Chisholm; Alan R Kimmel
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971
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