Literature DB >> 14681399

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

Philip E Bourne1, 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.   

Abstract

The Protein Data Bank (PDB; http://www.pdb.org) is the primary source of information on the 3D structure of biological macromolecules. The PDB's mandate is to disseminate this information in the most usable form and as widely as possible. The current query and distribution system is described and an alpha version of the future re-engineered system introduced.

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Year:  2004        PMID： 14681399      PMCID： PMC308830          DOI： 10.1093/nar/gkh096

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


  15 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.  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

3.  Clustering of highly homologous sequences to reduce the size of large protein databases.

Authors:  W Li; L Jaroszewski; A Godzik
Journal:  Bioinformatics       Date:  2001-03       Impact factor: 6.937

4.  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

5.  STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

Authors:  Goran Neshich; Roberto C Togawa; Adauto L Mancini; Paula R Kuser; Michel E B Yamagishi; Georgios Pappas; Wellington V Torres; Tharsis Fonseca e Campos; Leonardo L Ferreira; Fabio M Luna; Adilton G Oliveira; Ronald T Miura; Marcus K Inoue; Luiz G Horita; Dimas F de Souza; Fabiana Dominiquini; Alexandre Alvaro; Cleber S Lima; Fabio O Ogawa; Gabriel B Gomes; Juliana F Palandrani; Gabriela F dos Santos; Esther M de Freitas; Amanda R Mattiuz; Ivan C Costa; Celso L de Almeida; Savio Souza; Christian Baudet; Roberto H Higa
Journal:  Nucleic Acids Res       Date:  2003-07-01       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.  PQS: a protein quaternary structure file server.

Authors:  K Henrick; J M Thornton
Journal:  Trends Biochem Sci       Date:  1998-09       Impact factor: 13.807

8.  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

9.  Protein data representation and query using optimized data decomposition.

Authors:  I N Shindyalov; P E Bourne
Journal:  Comput Appl Biosci       Date:  1997-10

10.  An ontology driven architecture for derived representations of macromolecular structure.

Authors:  Douglas S Greer; John D Westbrook; Philip E Bourne
Journal:  Bioinformatics       Date:  2002-09       Impact factor: 6.937
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  43 in total

1.  STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.

Authors:  Matthias Heinig; Dmitrij Frishman
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  iMOT: an interactive package for the selection of spatially interacting motifs.

Authors:  A Bhaduri; G Pugalenthi; N Gupta; R Sowdhamini
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

3.  PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.

Authors:  Todd J Dolinsky; Jens E Nielsen; J Andrew McCammon; Nathan A Baker
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

4.  LOCnet and LOCtarget: sub-cellular localization for structural genomics targets.

Authors:  Rajesh Nair; Burkhard Rost
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

5.  Citing a Data Repository: A Case Study of the Protein Data Bank.

Authors:  Yi-Hung Huang; Peter W Rose; Chun-Nan Hsu
Journal:  PLoS One       Date:  2015-08-28       Impact factor: 3.240

6.  Prediction of volatile anesthetic binding sites in proteins.

Authors:  John H Streiff; Thomas W Allen; Elena Atanasova; Nenad Juranic; Slobodan Macura; Alan R Penheiter; Keith A Jones
Journal:  Biophys J       Date:  2006-07-28       Impact factor: 4.033

7.  A structural model for the large subunit of the mammalian mitochondrial ribosome.

Authors:  Jason A Mears; Manjuli R Sharma; Robin R Gutell; Amanda S McCook; Paul E Richardson; Thomas R Caulfield; Rajendra K Agrawal; Stephen C Harvey
Journal:  J Mol Biol       Date:  2006-02-10       Impact factor: 5.469

Review 8.  The proteome: structure, function and evolution.

Authors:  Keiran Fleming; Lawrence A Kelley; Suhail A Islam; Robert M MacCallum; Arne Muller; Florencio Pazos; Michael J E Sternberg
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-03-29       Impact factor: 6.237

9.  FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

Authors:  Michael Sarver; Craig L Zirbel; Jesse Stombaugh; Ali Mokdad; Neocles B Leontis
Journal:  J Math Biol       Date:  2007-08-11       Impact factor: 2.259

10.  On the modeling of snake venom serine proteinase interactions with benzamidine-based thrombin inhibitors.

Authors:  Elsa S Henriques; Nelson Fonseca; Maria João Ramos
Journal:  Protein Sci       Date:  2004-09       Impact factor: 6.725
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