Literature DB >> 25502191

Protein structure annotation resources.

Margaret J Gabanyi1, Helen M Berman.   

Abstract

A key reason three-dimensional (3-D) protein structures are annotated with supporting or derived information is to understand the molecular basis of protein function. To this end, protein structure annotation databases curate key facts and observations, based on community-accepted standards, about the ~100,000 3-D experimental protein structures to date. This review will introduce the primary structure repositories, databases, and value-added structural annotation databases, as well as the range of information they provide. The different levels of annotation data (primary vs. derived vs. inferred) and how they should all be considered accordingly will also be described.

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Year:  2015        PMID: 25502191      PMCID: PMC5586544          DOI: 10.1007/978-1-4939-2230-7_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  60 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.  ProtBuD: a database of biological unit structures of protein families and superfamilies.

Authors:  Qifang Xu; Adrian Canutescu; Zoran Obradovic; Roland L Dunbrack
Journal:  Bioinformatics       Date:  2006-10-02       Impact factor: 6.937

Review 3.  Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

Authors:  Jill Trewhella; Wayne A Hendrickson; Gerard J Kleywegt; Andrej Sali; Mamoru Sato; Torsten Schwede; Dmitri I Svergun; John A Tainer; John Westbrook; Helen M Berman
Journal:  Structure       Date:  2013-06-04       Impact factor: 5.006

4.  Recommendations of the wwPDB NMR Validation Task Force.

Authors:  Gaetano T Montelione; Michael Nilges; Ad Bax; Peter Güntert; Torsten Herrmann; Jane S Richardson; Charles D Schwieters; Wim F Vranken; Geerten W Vuister; David S Wishart; Helen M Berman; Gerard J Kleywegt; John L Markley
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

5.  The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.

Authors:  Alison L Cuff; Ian Sillitoe; Tony Lewis; Oliver C Redfern; Richard Garratt; Janet Thornton; Christine A Orengo
Journal:  Nucleic Acids Res       Date:  2008-11-07       Impact factor: 16.971

6.  The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

Authors:  Margaret J Gabanyi; Paul D Adams; Konstantin Arnold; Lorenza Bordoli; Lester G Carter; Judith Flippen-Andersen; Lida Gifford; Juergen Haas; Andrei Kouranov; William A McLaughlin; David I Micallef; Wladek Minor; Raship Shah; Torsten Schwede; Yi-Ping Tao; John D Westbrook; Matthew Zimmerman; Helen M Berman
Journal:  J Struct Funct Genomics       Date:  2011-04-07

7.  Outcome of the first electron microscopy validation task force meeting.

Authors:  Richard Henderson; Andrej Sali; Matthew L Baker; Bridget Carragher; Batsal Devkota; Kenneth H Downing; Edward H Egelman; Zukang Feng; Joachim Frank; Nikolaus Grigorieff; Wen Jiang; Steven J Ludtke; Ohad Medalia; Pawel A Penczek; Peter B Rosenthal; Michael G Rossmann; Michael F Schmid; Gunnar F Schröder; Alasdair C Steven; David L Stokes; John D Westbrook; Willy Wriggers; Huanwang Yang; Jasmine Young; Helen M Berman; Wah Chiu; Gerard J Kleywegt; Catherine L Lawson
Journal:  Structure       Date:  2012-02-08       Impact factor: 5.006

8.  3did: a catalog of domain-based interactions of known three-dimensional structure.

Authors:  Roberto Mosca; Arnaud Céol; Amelie Stein; Roger Olivella; Patrick Aloy
Journal:  Nucleic Acids Res       Date:  2013-09-29       Impact factor: 16.971

9.  The Protein Model Portal--a comprehensive resource for protein structure and model information.

Authors:  Juergen Haas; Steven Roth; Konstantin Arnold; Florian Kiefer; Tobias Schmidt; Lorenza Bordoli; Torsten Schwede
Journal:  Database (Oxford)       Date:  2013-04-26       Impact factor: 3.451

10.  DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research.

Authors:  Catherine Y Seiler; Jin G Park; Amit Sharma; Preston Hunter; Padmini Surapaneni; Casey Sedillo; James Field; Rhys Algar; Andrea Price; Jason Steel; Andrea Throop; Michael Fiacco; Joshua LaBaer
Journal:  Nucleic Acids Res       Date:  2013-11-12       Impact factor: 16.971

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