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      VirusMINT: a viral protein interaction database

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          Abstract

          Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network. The VirusMINT database ( http://mint.bio.uniroma2.it/virusmint/) aims at collecting all protein interactions between viral and human proteins reported in the literature. VirusMINT currently stores over 5000 interactions involving more than 490 unique viral proteins from more than 110 different viral strains. The whole data set can be easily queried through the search pages and the results can be displayed with a graphical viewer. The curation effort has focused on manuscripts reporting interactions between human proteins and proteins encoded by some of the most medically relevant viruses: papilloma viruses, human immunodeficiency virus 1, Epstein–Barr virus, hepatitis B virus, hepatitis C virus, herpes viruses and Simian virus 40.

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          The Universal Protein Resource (UniProt)

          emmanuel boutet, Claire O'Donovan (2008)
          The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. The UniProt Consortium is a collaboration between the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Knowledgebase, the UniProt Reference Clusters, the UniProt Archive and the UniProt Metagenomic and Environmental Sequences database. UniProt is updated and distributed every three weeks, and can be accessed online for searches or download at http://www.uniprot.org.
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            MINT: the Molecular INTeraction database

            Andrew Chatr-aryamontri, Arnaud Ceol, Luisa Palazzi … (2006)
            The Molecular INTeraction database (MINT, ) aims at storing, in a structured format, information about molecular interactions (MIs) by extracting experimental details from work published in peer-reviewed journals. At present the MINT team focuses the curation work on physical interactions between proteins. Genetic or computationally inferred interactions are not included in the database. Over the past four years MINT has undergone extensive revision. The new version of MINT is based on a completely remodeled database structure, which offers more efficient data exploration and analysis, and is characterized by entries with a richer annotation. Over the past few years the number of curated physical interactions has soared to over 95 000. The whole dataset can be freely accessed online in both interactive and batch modes through web-based interfaces and an FTP server. MINT now includes, as an integrated addition, HomoMINT, a database of interactions between human proteins inferred from experiments with ortholog proteins in model organisms ().
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              IntAct—open source resource for molecular interaction data

              S. Kerrien, Y. Alam-Faruque, Gloria Aranda … (2006)
              IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126 000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from .
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: January 2009
                Publication date (Print): January 2009
                Publication date (Electronic): 30 October 2008
                Publication date PMC-release: 30 October 2008
                Volume: 37
                Issue: Database issue , Database issue
                Pages: D669-D673
                Affiliations
                1Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, 2IRCCS Fondazione Santa Lucia, 00143 Rome, 3Department of Cell Biology, University of Calabria, Via P. Bucci, Rende (CS) Italy and 4Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +39 0672594315; Fax: +39 062023500; Email: cesareni@ 123456uniroma2.it

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                Article
                Publisher ID: gkn739
                DOI: 10.1093/nar/gkn739
                PMC ID: 2686573
                PubMed ID: 18974184
                SO-VID: 5664dc68-c30e-4bb4-809d-9fa38504c214
                Copyright © © 2008 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 13 August 2008
                Date revision received : 20 September 2008
                Date accepted : 2 October 2008
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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