Literature DB >> 12519985

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.

Shuai Weng1, Qing Dong, Rama Balakrishnan, Karen Christie, Maria Costanzo, Kara Dolinski, Selina S Dwight, Stacia Engel, Dianna G Fisk, Eurie Hong, Laurie Issel-Tarver, Anand Sethuraman, Chandra Theesfeld, Rey Andrada, Gail Binkley, Christopher Lane, Mark Schroeder, David Botstein, J Michael Cherry.   

Abstract

The Saccharomyces Genome Database (SGD: http://genome-www.stanford.edu/Saccharomyces/) has recently developed new resources to provide more complete information about proteins from the budding yeast Saccharomyces cerevisiae. The PDB Homologs page provides structural information from the Protein Data Bank (PDB) about yeast proteins and/or their homologs. SGD has also created a resource that utilizes the eMOTIF database for motif information about a given protein. A third new resource is the Protein Information page, which contains protein physical and chemical properties, such as molecular weight and hydropathicity scores, predicted from the translated ORF sequence.

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Year:  2003        PMID: 12519985      PMCID: PMC165501          DOI: 10.1093/nar/gkg054

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


  7 in total

1.  The EMOTIF database.

Authors:  J Y Huang; D L Brutlag
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

3.  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

4.  Integrating functional genomic information into the Saccharomyces genome database.

Authors:  C A Ball; K Dolinski; S S Dwight; M A Harris; L Issel-Tarver; A Kasarskis; C R Scafe; G Sherlock; G Binkley; H Jin; M Kaloper; S D Orr; M Schroeder; S Weng; Y Zhu; D Botstein; J M Cherry
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

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.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

Authors:  P M Sharp; W H Li
Journal:  Nucleic Acids Res       Date:  1987-02-11       Impact factor: 16.971

7.  Identification of common molecular subsequences.

Authors:  T F Smith; M S Waterman
Journal:  J Mol Biol       Date:  1981-03-25       Impact factor: 5.469

  7 in total
  32 in total

1.  Protein complexes and functional modules in molecular networks.

Authors:  Victor Spirin; Leonid A Mirny
Journal:  Proc Natl Acad Sci U S A       Date:  2003-09-29       Impact factor: 11.205

2.  RPG: the Ribosomal Protein Gene database.

Authors:  Akihiro Nakao; Maki Yoshihama; Naoya Kenmochi
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  GeneDB: a resource for prokaryotic and eukaryotic organisms.

Authors:  Christiane Hertz-Fowler; Chris S Peacock; Valerie Wood; Martin Aslett; Arnaud Kerhornou; Paul Mooney; Adrian Tivey; Matthew Berriman; Neil Hall; Kim Rutherford; Julian Parkhill; Alasdair C Ivens; Marie-Adele Rajandream; Bart Barrell
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  IntAct: an open source molecular interaction database.

Authors:  Henning Hermjakob; Luisa Montecchi-Palazzi; Chris Lewington; Sugath Mudali; Samuel Kerrien; Sandra Orchard; Martin Vingron; Bernd Roechert; Peter Roepstorff; Alfonso Valencia; Hanah Margalit; John Armstrong; Amos Bairoch; Gianni Cesareni; David Sherman; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  MetaCyc: a multiorganism database of metabolic pathways and enzymes.

Authors:  Cynthia J Krieger; Peifen Zhang; Lukas A Mueller; Alfred Wang; Suzanne Paley; Martha Arnaud; John Pick; Seung Y Rhee; Peter D Karp
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms.

Authors:  Günther Zehetner
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 7.  The Ensembl core software libraries.

Authors:  Arne Stabenau; Graham McVicker; Craig Melsopp; Glenn Proctor; Michele Clamp; Ewan Birney
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

8.  Ty1 mobilizes subtelomeric Y' elements in telomerase-negative Saccharomyces cerevisiae survivors.

Authors:  Patrick H Maxwell; Candice Coombes; Alison E Kenny; Joseph F Lawler; Jef D Boeke; M Joan Curcio
Journal:  Mol Cell Biol       Date:  2004-11       Impact factor: 4.272

9.  Next generation software for functional trend analysis.

Authors:  Gabriel F Berriz; John E Beaver; Can Cenik; Murat Tasan; Frederick P Roth
Journal:  Bioinformatics       Date:  2009-08-28       Impact factor: 6.937

10.  GermOnline, a cross-species community knowledgebase on germ cell differentiation.

Authors:  C Wiederkehr; R Basavaraj; C Sarrauste de Menthière; L Hermida; R Koch; U Schlecht; A Amon; S Brachat; M Breitenbach; P Briza; S Caburet; M Cherry; R Davis; A Deutschbauer; H G Dickinson; T Dumitrescu; M Fellous; A Goldman; J A Grootegoed; R Hawley; R Ishii; B Jégou; R J Kaufman; F Klein; N Lamb; B Maro; K Nasmyth; A Nicolas; T Orr-Weaver; P Philippsen; C Pineau; K P Rabitsch; V Reinke; H Roest; W Saunders; M Schröder; T Schedl; M Siep; A Villeneuve; D J Wolgemuth; M Yamamoto; D Zickler; R E Esposito; M Primig
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

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