MPIDB: the Microbial Protein Interaction Database

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2008 Jun 17

PMID 18556668

Citations 55

Authors

Johannes Goll

Seesandra V Rajagopala

Shen C Shiau

Hank Wu

Brian T Lamb

Peter Uetz

Affiliations

Soon will be listed here.

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/

Citing Articles

Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration.

Fang T, Szklarczyk D, Hachilif R, von Mering C Sci Rep. 2024; 14(1):6009.

PMID: 38472223 PMC: 10933411. DOI: 10.1038/s41598-024-55655-9.

Finding melanoma drugs through a probabilistic knowledge graph.

McCusker J, Dumontier M, Yan R, He S, Dordick J, McGuinness D PeerJ Comput Sci. 2023; 3:e106.

PMID: 37133296 PMC: 10151034. DOI: 10.7717/peerj-cs.106.

Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data.

Hollander M, Do T, Will T, Helms V Front Bioinform. 2022; 1:724297.

PMID: 36303788 PMC: 9581068. DOI: 10.3389/fbinf.2021.724297.

The Landscape of Virus-Host Protein-Protein Interaction Databases.

Valiente G Front Microbiol. 2022; 13:827742.

PMID: 35910656 PMC: 9335289. DOI: 10.3389/fmicb.2022.827742.

ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions.

Tayal S, Bhatia V, Mehrotra T, Bhatnagar S Amino Acids. 2022; 54(6):923-934.

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References

Salwinski L, Miller C, Smith A, Pettit F, Bowie J, Eisenberg D . The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2003; 32(Database issue):D449-51. PMC: 308820. DOI: 10.1093/nar/gkh086. View

. The universal protein resource (UniProt). Nucleic Acids Res. 2007; 36(Database issue):D190-5. PMC: 2238893. DOI: 10.1093/nar/gkm895. View

Alfarano C, Andrade C, Anthony K, Bahroos N, Bajec M, Bantoft K . The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 2004; 33(Database issue):D418-24. PMC: 540005. DOI: 10.1093/nar/gki051. View

Stein A, Russell R, Aloy P . 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 2004; 33(Database issue):D413-7. PMC: 539991. DOI: 10.1093/nar/gki037. View

Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G . MINT: a Molecular INTeraction database. FEBS Lett. 2002; 513(1):135-40. DOI: 10.1016/s0014-5793(01)03293-8. View

Finn R, Marshall M, Bateman A . iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics. 2004; 21(3):410-2. DOI: 10.1093/bioinformatics/bti011. View

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn A, Vinod N . Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007; 5:44. PMC: 2189715. DOI: 10.1186/1741-7007-5-44. View

Titz B, Rajagopala S, Goll J, Hauser R, McKevitt M, Palzkill T . The binary protein interactome of Treponema pallidum--the syphilis spirochete. PLoS One. 2008; 3(5):e2292. PMC: 2386257. DOI: 10.1371/journal.pone.0002292. View

Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C . IntAct--open source resource for molecular interaction data. Nucleic Acids Res. 2006; 35(Database issue):D561-5. PMC: 1751531. DOI: 10.1093/nar/gkl958. View

10.

Jeong H, Mason S, Barabasi A, Oltvai Z . Lethality and centrality in protein networks. Nature. 2001; 411(6833):41-2. DOI: 10.1038/35075138. View

11.

von Mering C, Jensen L, Kuhn M, Chaffron S, Doerks T, Kruger B . STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2006; 35(Database issue):D358-62. PMC: 1669762. DOI: 10.1093/nar/gkl825. View