Literature DB >> 11465066

Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences.

R Apweiler1.   

Abstract

With the rapid growth of sequence databases, there is an increasing need for reliable functional characterisation and annotation of newly predicted proteins. To cope with such large data volumes, faster and more effective means of protein sequence characterisation and annotation are required. One promising approach is automatic large-scale functional characterisation and annotation, which is generated with limited human interaction. However, such an approach is heavily dependent on reliable data sources. The SWISS-PROT protein sequence database plays an essential role here owing to its high level of functional information.

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Year:  2001        PMID: 11465066     DOI: 10.1093/bib/2.1.9

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  17 in total

1.  The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Authors:  Evelyn Camon; Michele Magrane; Daniel Barrell; David Binns; Wolfgang Fleischmann; Paul Kersey; Nicola Mulder; Tom Oinn; John Maslen; Anthony Cox; Rolf Apweiler
Journal:  Genome Res       Date:  2003-03-12       Impact factor: 9.043

2.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.

Authors:  Brigitte Boeckmann; Amos Bairoch; Rolf Apweiler; Marie-Claude Blatter; Anne Estreicher; Elisabeth Gasteiger; Maria J Martin; Karine Michoud; Claire O'Donovan; Isabelle Phan; Sandrine Pilbout; Michel Schneider
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

3.  The European Bioinformatics Institute's data resources.

Authors:  Catherine Brooksbank; Evelyn Camon; Midori A Harris; Michele Magrane; Maria Jesus Martin; Nicola Mulder; Claire O'Donovan; Helen Parkinson; Mary Ann Tuli; Rolf Apweiler; Ewan Birney; Alvis Brazma; Kim Henrick; Rodrigo Lopez; Guenter Stoesser; Peter Stoehr; Graham Cameron
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  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

5.  Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Authors:  Selina S Dwight; Midori A Harris; Kara Dolinski; Catherine A Ball; Gail Binkley; Karen R Christie; Dianna G Fisk; Laurie Issel-Tarver; Mark Schroeder; Gavin Sherlock; Anand Sethuraman; Shuai Weng; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  Prediction of carbohydrate-binding proteins from sequences using support vector machines.

Authors:  Seizi Someya; Masanori Kakuta; Mizuki Morita; Kazuya Sumikoshi; Wei Cao; Zhenyi Ge; Osamu Hirose; Shugo Nakamura; Tohru Terada; Kentaro Shimizu
Journal:  Adv Bioinformatics       Date:  2010-09-27

7.  New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

Authors:  Ian Sillitoe; Alison L Cuff; Benoit H Dessailly; Natalie L Dawson; Nicholas Furnham; David Lee; Jonathan G Lees; Tony E Lewis; Romain A Studer; Robert Rentzsch; Corin Yeats; Janet M Thornton; Christine A Orengo
Journal:  Nucleic Acids Res       Date:  2012-11-29       Impact factor: 16.971

8.  Automated quantitative assessment of proteins' biological function in protein knowledge bases.

Authors:  Gabriele Mayr; Günter Lepperdinger; Peter Lackner
Journal:  Adv Bioinformatics       Date:  2008-06-30

9.  mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines.

Authors:  Shibiao Wan; Man-Wai Mak; Sun-Yuan Kung
Journal:  BMC Bioinformatics       Date:  2012-11-06       Impact factor: 3.169

10.  TransportTP: a two-phase classification approach for membrane transporter prediction and characterization.

Authors:  Haiquan Li; Vagner A Benedito; Michael K Udvardi; Patrick Xuechun Zhao
Journal:  BMC Bioinformatics       Date:  2009-12-14       Impact factor: 3.169

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