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Literature DB >> 14681454

The Database of Interacting Proteins: 2004 update.

Lukasz Salwinski¹, Christopher S Miller, Adam J Smith, Frank K Pettit, James U Bowie, David Eisenberg.

Abstract

The Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu) aims to integrate the diverse body of experimental evidence on protein-protein interactions into a single, easily accessible online database. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks.

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Year: 2004 PMID： 14681454 PMCID： PMC308820 DOI： 10.1093/nar/gkh086

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

17 in total

1. DIP: the database of interacting proteins.

Authors: I Xenarios; D W Rice; L Salwinski; M K Baron; E M Marcotte; D Eisenberg
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. Is there a bias in proteome research?

Authors: R Mrowka; A Patzak; H Herzel
Journal: Genome Res Date: 2001-12 Impact factor: 9.043

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. Comparative assessment of large-scale data sets of protein-protein interactions.

Authors: Christian von Mering; Roland Krause; Berend Snel; Michael Cornell; Stephen G Oliver; Stanley Fields; Peer Bork
Journal: Nature Date: 2002-05-08 Impact factor: 49.962

5. Functional organization of the yeast proteome by systematic analysis of protein complexes.

Authors: Anne-Claude Gavin; Markus Bösche; Roland Krause; Paola Grandi; Martina Marzioch; Andreas Bauer; Jörg Schultz; Jens M Rick; Anne-Marie Michon; Cristina-Maria Cruciat; Marita Remor; Christian Höfert; Malgorzata Schelder; Miro Brajenovic; Heinz Ruffner; Alejandro Merino; Karin Klein; Manuela Hudak; David Dickson; Tatjana Rudi; Volker Gnau; Angela Bauch; Sonja Bastuck; Bettina Huhse; Christina Leutwein; Marie-Anne Heurtier; Richard R Copley; Angela Edelmann; Erich Querfurth; Vladimir Rybin; Gerard Drewes; Manfred Raida; Tewis Bouwmeester; Peer Bork; Bertrand Seraphin; Bernhard Kuster; Gitte Neubauer; Giulio Superti-Furga
Journal: Nature Date: 2002-01-10 Impact factor: 49.962

6. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.

Authors: Yuen Ho; Albrecht Gruhler; Adrian Heilbut; Gary D Bader; Lynda Moore; Sally-Lin Adams; Anna Millar; Paul Taylor; Keiryn Bennett; Kelly Boutilier; Lingyun Yang; Cheryl Wolting; Ian Donaldson; Søren Schandorff; Juanita Shewnarane; Mai Vo; Joanne Taggart; Marilyn Goudreault; Brenda Muskat; Cris Alfarano; Danielle Dewar; Zhen Lin; Katerina Michalickova; Andrew R Willems; Holly Sassi; Peter A Nielsen; Karina J Rasmussen; Jens R Andersen; Lene E Johansen; Lykke H Hansen; Hans Jespersen; Alexandre Podtelejnikov; Eva Nielsen; Janne Crawford; Vibeke Poulsen; Birgitte D Sørensen; Jesper Matthiesen; Ronald C Hendrickson; Frank Gleeson; Tony Pawson; Michael F Moran; Daniel Durocher; Matthias Mann; Christopher W V Hogue; Daniel Figeys; Mike Tyers
Journal: Nature Date: 2002-01-10 Impact factor: 49.962

7. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.

Authors: Ioannis Xenarios; Lukasz Salwínski; Xiaoqun Joyce Duan; Patrick Higney; Sul-Min Kim; David Eisenberg
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

8. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.

Authors: P Uetz; L Giot; G Cagney; T A Mansfield; R S Judson; J R Knight; D Lockshon; V Narayan; M Srinivasan; P Pochart; A Qureshi-Emili; Y Li; B Godwin; D Conover; T Kalbfleisch; G Vijayadamodar; M Yang; M Johnston; S Fields; J M Rothberg
Journal: Nature Date: 2000-02-10 Impact factor: 49.962

Review 9. MINT: a Molecular INTeraction database.

Authors: Andreas Zanzoni; Luisa Montecchi-Palazzi; Michele Quondam; Gabriele Ausiello; Manuela Helmer-Citterich; Gianni Cesareni
Journal: FEBS Lett Date: 2002-02-20 Impact factor: 4.124

10. A comprehensive two-hybrid analysis to explore the yeast protein interactome.

Authors: T Ito; T Chiba; R Ozawa; M Yoshida; M Hattori; Y Sakaki
Journal: Proc Natl Acad Sci U S A Date: 2001-03-13 Impact factor: 11.205

811 in total

1. Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology.

Authors: Renu Goel; Babylakshmi Muthusamy; Akhilesh Pandey; T S Keshava Prasad
Journal: Mol Biotechnol Date: 2011-05 Impact factor: 2.695

2. Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.

Authors: Matthew J Betts; Qianhao Lu; YingYing Jiang; Armin Drusko; Oliver Wichmann; Mathias Utz; Ilse A Valtierra-Gutiérrez; Matthias Schlesner; Natalie Jaeger; David T Jones; Stefan Pfister; Peter Lichter; Roland Eils; Reiner Siebert; Peer Bork; Gordana Apic; Anne-Claude Gavin; Robert B Russell
Journal: Nucleic Acids Res Date: 2014-11-11 Impact factor: 16.971

3. Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test.

Authors: Chao Wu; Fan Zhang; Xia Li; Shihua Zhang; Jiang Li; Fei Su; Kongning Li; Yuqing Yan
Journal: BMC Syst Biol Date: 2010-06-10

The Database of Interacting Proteins: 2004 update.

1. DIP: the database of interacting proteins.

2. Is there a bias in proteome research?

3. The Protein Data Bank: unifying the archive.

4. Comparative assessment of large-scale data sets of protein-protein interactions.

5. Functional organization of the yeast proteome by systematic analysis of protein complexes.

6. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.

7. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.

8. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.

Review 9. MINT: a Molecular INTeraction database.

10. A comprehensive two-hybrid analysis to explore the yeast protein interactome.

1. Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology.

2. Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.

3. Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test.

4. Exploration of biological network centralities with CentiBiN.

5. PathBLAST: a tool for alignment of protein interaction networks.

Review 6. Charting gene regulatory networks: strategies, challenges and perspectives.

Review 7. 'Conserved hypothetical' proteins: prioritization of targets for experimental study.

8. IMID: integrated molecular interaction database.

9. System approaches reveal the molecular networks involved in neural stem cell differentiation.

10. Information flow in interaction networks II: channels, path lengths, and potentials.