Literature DB >> 14764547

PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt.

Andrew C R Martin1.   

Abstract

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.

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Year:  2004        PMID： 14764547     DOI： 10.1093/bioinformatics/bth048

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


  17 in total

1.  Prediction and experimental validation of enzyme substrate specificity in protein structures.

Authors:  Shivas R Amin; Serkan Erdin; R Matthew Ward; Rhonald C Lua; Olivier Lichtarge
Journal:  Proc Natl Acad Sci U S A       Date:  2013-10-21       Impact factor: 11.205

Review 2.  Toward mechanistic classification of enzyme functions.

Authors:  Daniel E Almonacid; Patricia C Babbitt
Journal:  Curr Opin Chem Biol       Date:  2011-04-12       Impact factor: 8.822

3.  Towards site-based protein functional annotations.

Authors:  Seak Fei Lei; Jun Huan
Journal:  Int J Data Min Bioinform       Date:  2010       Impact factor: 0.667

4.  Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

Authors:  Daniel E Almonacid; Emmanuel R Yera; John B O Mitchell; Patricia C Babbitt
Journal:  PLoS Comput Biol       Date:  2010-03-12       Impact factor: 4.475

5.  Metal ions in biological catalysis: from enzyme databases to general principles.

Authors:  Claudia Andreini; Ivano Bertini; Gabriele Cavallaro; Gemma L Holliday; Janet M Thornton
Journal:  J Biol Inorg Chem       Date:  2008-07-05       Impact factor: 3.358

6.  PoSSuM: a database of similar protein-ligand binding and putative pockets.

Authors:  Jun-Ichi Ito; Yasuo Tabei; Kana Shimizu; Koji Tsuda; Kentaro Tomii
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

7.  MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.

Authors:  Gemma L Holliday; Daniel E Almonacid; Gail J Bartlett; Noel M O'Boyle; James W Torrance; Peter Murray-Rust; John B O Mitchell; Janet M Thornton
Journal:  Nucleic Acids Res       Date:  2006-11-01       Impact factor: 16.971

8.  Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB).

Authors:  Antoni Hermoso; Jordi Espadaler; E Enrique Querol; Francesc X Aviles; Michael J E Sternberg; Baldomero Oliva; Narcis Fernandez-Fuentes
Journal:  Bioinform Biol Insights       Date:  2009-11-24

9.  FLORA: a novel method to predict protein function from structure in diverse superfamilies.

Authors:  Oliver C Redfern; Benoît H Dessailly; Timothy J Dallman; Ian Sillitoe; Christine A Orengo
Journal:  PLoS Comput Biol       Date:  2009-08-28       Impact factor: 4.475

10.  PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

Authors:  Marcin von Grotthuss; Dariusz Plewczynski; Krzysztof Ginalski; Leszek Rychlewski; Eugene I Shakhnovich
Journal:  BMC Bioinformatics       Date:  2006-02-06       Impact factor: 3.169
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