Literature DB >> 15509603

PDBML: the representation of archival macromolecular structure data in XML.

John Westbrook1, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M Berman.   

Abstract

SUMMARY: The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files.

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Year:  2004        PMID: 15509603     DOI: 10.1093/bioinformatics/bti082

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  51 in total

1.  Generation of a consensus protein domain dictionary.

Authors:  R Dustin Schaeffer; Amanda L Jonsson; Andrew M Simms; Valerie Daggett
Journal:  Bioinformatics       Date:  2010-11-09       Impact factor: 6.937

2.  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

3.  AllerML: markup language for allergens.

Authors:  Ovidiu Ivanciuc; Steven M Gendel; Trevor D Power; Catherine H Schein; Werner Braun
Journal:  Regul Toxicol Pharmacol       Date:  2011-03-21       Impact factor: 3.271

4.  The RNA Ontology Consortium: an open invitation to the RNA community.

Authors:  Neocles B Leontis; Russ B Altman; Helen M Berman; Steven E Brenner; James W Brown; David R Engelke; Stephen C Harvey; Stephen R Holbrook; Fabrice Jossinet; Suzanna E Lewis; François Major; David H Mathews; Jane S Richardson; James R Williamson; Eric Westhof
Journal:  RNA       Date:  2006-02-16       Impact factor: 4.942

5.  The Extensible Neuroimaging Archive Toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data.

Authors:  Daniel S Marcus; Timothy R Olsen; Mohana Ramaratnam; Randy L Buckner
Journal:  Neuroinformatics       Date:  2007

Review 6.  Data deposition and annotation at the worldwide protein data bank.

Authors:  Shuchismita Dutta; Kyle Burkhardt; Jasmine Young; Ganesh J Swaminathan; Takanori Matsuura; Kim Henrick; Haruki Nakamura; Helen M Berman
Journal:  Mol Biotechnol       Date:  2008-12-10       Impact factor: 2.695

7.  3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.

Authors:  Xiang-Jun Lu; Wilma K Olson
Journal:  Nat Protoc       Date:  2008       Impact factor: 13.491

Review 8.  Protein Bioinformatics Databases and Resources.

Authors:  Chuming Chen; Hongzhan Huang; Cathy H Wu
Journal:  Methods Mol Biol       Date:  2017

9.  Statistical analysis of interface similarity in crystals of homologous proteins.

Authors:  Qifang Xu; Adrian A Canutescu; Guoli Wang; Maxim Shapovalov; Zoran Obradovic; Roland L Dunbrack
Journal:  J Mol Biol       Date:  2008-06-07       Impact factor: 5.469

10.  An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases.

Authors:  Brian Weitzner; Thomas Meehan; Qifang Xu; Roland L Dunbrack
Journal:  Proteins       Date:  2009-05-01
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