Literature DB >> 18556668

MPIDB: the microbial protein interaction database.

Johannes Goll1, Seesandra V Rajagopala, Shen C Shiau, Hank Wu, Brian T Lamb, Peter Uetz.   

Abstract

SUMMARY: The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 22,530 experimentally determined interactions among proteins of 191 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 24,060 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 8150 additional evidences based on interaction conservation, co-purification and 3D domain contacts (iPfam, 3did). AVAILABILITY: http://www.jcvi.org/mpidb/

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Year:  2008        PMID： 18556668      PMCID： PMC2638870          DOI： 10.1093/bioinformatics/btn285

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


  11 in total

1.  Lethality and centrality in protein networks.

Authors:  H Jeong; S P Mason; A L Barabási; Z N Oltvai
Journal:  Nature       Date:  2001-05-03       Impact factor: 49.962

2.  The Database of Interacting Proteins: 2004 update.

Authors:  Lukasz Salwinski; Christopher S Miller; Adam J Smith; Frank K Pettit; James U Bowie; David Eisenberg
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions.

Authors:  Robert D Finn; Mhairi Marshall; Alex Bateman
Journal:  Bioinformatics       Date:  2004-09-07       Impact factor: 6.937

Review 4.  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

5.  IntAct--open source resource for molecular interaction data.

Authors:  S Kerrien; Y Alam-Faruque; B Aranda; I Bancarz; A Bridge; C Derow; E Dimmer; M Feuermann; A Friedrichsen; R Huntley; C Kohler; J Khadake; C Leroy; A Liban; C Lieftink; L Montecchi-Palazzi; S Orchard; J Risse; K Robbe; B Roechert; D Thorneycroft; Y Zhang; R Apweiler; H Hermjakob
Journal:  Nucleic Acids Res       Date:  2006-12-01       Impact factor: 16.971

6.  3did: interacting protein domains of known three-dimensional structure.

Authors:  Amelie Stein; Robert B Russell; Patrick Aloy
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

7.  The Biomolecular Interaction Network Database and related tools 2005 update.

Authors:  C Alfarano; C E Andrade; K Anthony; N Bahroos; M Bajec; K Bantoft; D Betel; B Bobechko; K Boutilier; E Burgess; K Buzadzija; R Cavero; C D'Abreo; I Donaldson; D Dorairajoo; M J Dumontier; M R Dumontier; V Earles; R Farrall; H Feldman; E Garderman; Y Gong; R Gonzaga; V Grytsan; E Gryz; V Gu; E Haldorsen; A Halupa; R Haw; A Hrvojic; L Hurrell; R Isserlin; F Jack; F Juma; A Khan; T Kon; S Konopinsky; V Le; E Lee; S Ling; M Magidin; J Moniakis; J Montojo; S Moore; B Muskat; I Ng; J P Paraiso; B Parker; G Pintilie; R Pirone; J J Salama; S Sgro; T Shan; Y Shu; J Siew; D Skinner; K Snyder; R Stasiuk; D Strumpf; B Tuekam; S Tao; Z Wang; M White; R Willis; C Wolting; S Wong; A Wrong; C Xin; R Yao; B Yates; S Zhang; K Zheng; T Pawson; B F F Ouellette; C W V Hogue
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

8.  The universal protein resource (UniProt).

Authors: 
Journal:  Nucleic Acids Res       Date:  2007-11-27       Impact factor: 16.971

9.  Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Authors:  Samuel Kerrien; Sandra Orchard; Luisa Montecchi-Palazzi; Bruno Aranda; Antony F Quinn; Nisha Vinod; Gary D Bader; Ioannis Xenarios; Jérôme Wojcik; David Sherman; Mike Tyers; John J Salama; Susan Moore; Arnaud Ceol; Andrew Chatr-Aryamontri; Matthias Oesterheld; Volker Stümpflen; Lukasz Salwinski; Jason Nerothin; Ethan Cerami; Michael E Cusick; Marc Vidal; Michael Gilson; John Armstrong; Peter Woollard; Christopher Hogue; David Eisenberg; Gianni Cesareni; Rolf Apweiler; Henning Hermjakob
Journal:  BMC Biol       Date:  2007-10-09       Impact factor: 7.431

10.  The binary protein interactome of Treponema pallidum--the syphilis spirochete.

Authors:  Björn Titz; Seesandra V Rajagopala; Johannes Goll; Roman Häuser; Matthew T McKevitt; Timothy Palzkill; Peter Uetz
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  48 in total

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Journal:  RNA       Date:  2010-09-15       Impact factor: 4.942

2.  Identifying gene interaction networks.

Authors:  Gurkan Bebek
Journal:  Methods Mol Biol       Date:  2012

3.  Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Authors:  Robin Haw; Henning Hermjakob; Peter D'Eustachio; Lincoln Stein
Journal:  Proteomics       Date:  2011-09       Impact factor: 3.984

4.  MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions.

Authors:  Seesandra V Rajagopala; Johannes Goll; N D Deve Gowda; Kumar C Sunil; Björn Titz; Arnab Mukherjee; Sharmila S Mary; Naresh Raviswaran; Chetan S Poojari; Srinivas Ramachandra; Svetlana Shtivelband; Stephen M Blazie; Julia Hofmann; Peter Uetz
Journal:  Bioinformatics       Date:  2008-09-11       Impact factor: 6.937

5.  Studying protein complexes by the yeast two-hybrid system.

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Journal:  Methods       Date:  2012-07-24       Impact factor: 3.608

6.  Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins.

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Journal:  Proteomics       Date:  2009-12       Impact factor: 3.984

7.  Pathema: a clade-specific bioinformatics resource center for pathogen research.

Authors:  Lauren M Brinkac; Tanja Davidsen; Erin Beck; Anuradha Ganapathy; Elisabet Caler; Robert J Dodson; A Scott Durkin; Derek M Harkins; Hernan Lorenzi; Ramana Madupu; Yinong Sebastian; Susmita Shrivastava; Mathangi Thiagarajan; Joshua Orvis; Jaideep P Sundaram; Jonathon Crabtree; Kevin Galens; Yongmei Zhao; Jason M Inman; Robert Montgomery; Seth Schobel; Kevin Galinsky; David M Tanenbaum; Adam Resnick; Nikhat Zafar; Owen White; Granger Sutton
Journal:  Nucleic Acids Res       Date:  2009-10-20       Impact factor: 16.971

8.  A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.

Authors:  Lope A Flórez; Sebastian F Roppel; Arne G Schmeisky; Christoph R Lammers; Jörg Stülke
Journal:  Database (Oxford)       Date:  2009-09-17       Impact factor: 3.451

9.  SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studies.

Authors:  Anu Chakicherla; Carol L Ecale Zhou; Martha Ligon Dang; Virginia Rodriguez; J Norman Hansen; Adam Zemla
Journal:  PLoS Comput Biol       Date:  2009-06-05       Impact factor: 4.475

10.  DASMIweb: online integration, analysis and assessment of distributed protein interaction data.

Authors:  Hagen Blankenburg; Fidel Ramírez; Joachim Büch; Mario Albrecht
Journal:  Nucleic Acids Res       Date:  2009-06-05       Impact factor: 16.971
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