Literature DB >> 11125095

The PDB data uniformity project.

T N Bhat1, P Bourne, Z Feng, G Gilliland, S Jain, V Ravichandran, B Schneider, K Schneider, N Thanki, H Weissig, J Westbrook, H M Berman.   

Abstract

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the data uniformity project that is underway to address the inconsistency in PDB data.

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Year:  2001        PMID： 11125095      PMCID： PMC29799          DOI： 10.1093/nar/29.1.214

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


  7 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 structural basis of ribosome activity in peptide bond synthesis.

Authors:  P Nissen; J Hansen; N Ban; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

4.  The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.

Authors:  H M Berman; W K Olson; D L Beveridge; J Westbrook; A Gelbin; T Demeny; S H Hsieh; A R Srinivasan; B Schneider
Journal:  Biophys J       Date:  1992-09       Impact factor: 4.033

5.  Database resources of the National Center for Biotechnology Information.

Authors:  D L Wheeler; C Chappey; A E Lash; D D Leipe; T L Madden; G D Schuler; T A Tatusova; B A Rapp
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

6.  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

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
  7 in total
  22 in total

1.  A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm.

Authors:  I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  The Protein Data Bank: unifying the archive.

Authors:  John Westbrook; 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
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets.

Authors:  Chantal Abergel; Bruno Coutard; Deborah Byrne; Sabine Chenivesse; Jean-Baptiste Claude; Céline Deregnaucourt; Thierry Fricaux; Celine Gianesini-Boutreux; Sandra Jeudy; Régine Lebrun; Caroline Maza; Cédric Notredame; Olivier Poirot; Karsten Suhre; Majorie Varagnol; Jean-Michel Claverie
Journal:  J Struct Funct Genomics       Date:  2003

4.  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

5.  Plant protein annotation in the UniProt Knowledgebase.

Authors:  Michel Schneider; Amos Bairoch; Cathy H Wu; Rolf Apweiler
Journal:  Plant Physiol       Date:  2005-05       Impact factor: 8.340

6.  Recall and bias of retrieving gene expression microarray datasets through PubMed identifiers.

Authors:  Heather Piwowar; Wendy Chapman
Journal:  J Biomed Discov Collab       Date:  2010-03-28

7.  RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

Authors:  Stephen K Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V Crichlow; Jose M Duarte; Shuchismita Dutta; Maryam Fayazi; Zukang Feng; Justin W Flatt; Sai J Ganesan; David S Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranovic; Jeremy Henry; Brian P Hudson; Catherine L Lawson; Yuhe Liang; Robert Lowe; Ezra Peisach; Irina Persikova; Dennis W Piehl; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Brinda Vallat; Maria Voigt; John D Westbrook; Shamara Whetstone; Jasmine Y Young; Christine Zardecki
Journal:  Protein Sci       Date:  2021-11-06       Impact factor: 6.725

8.  Molecular modeling of the three-dimensional structure of GLP-1R and its interactions with several agonists.

Authors:  Fu Lin; Renxiao Wang
Journal:  J Mol Model       Date:  2008-10-22       Impact factor: 1.810

9.  Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.

Authors:  Wolfgang F Bluhm; Bojan Beran; Chunxiao Bi; Dimitris Dimitropoulos; Andreas Prlic; Gregory B Quinn; Peter W Rose; Chaitali Shah; Jasmine Young; Benjamin Yukich; Helen M Berman; Philip E Bourne
Journal:  Database (Oxford)       Date:  2011-03-07       Impact factor: 3.451

10.  PISCES: recent improvements to a PDB sequence culling server.

Authors:  Guoli Wang; Roland L Dunbrack
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971
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