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      DOMINO: a database of domain–peptide interactions

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          Abstract

          Many protein interactions are mediated by small protein modules binding to short linear peptides. DOMINO ( http://mint.bio.uniroma2.it/domino/) is an open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. DOMINO can be searched with a versatile search tool and the interaction networks can be visualized with a convenient graphic display applet that explicitly identifies the domains/sites involved in the interactions.

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

          I Xenarios (2002)
          The Database of Interacting Proteins (DIP: http://dip.doe-mbi.ucla.edu) is a database that documents experimentally determined protein-protein interactions. It provides the scientific community with an integrated set of tools for browsing and extracting information about protein interaction networks. As of September 2001, the DIP catalogs approximately 11 000 unique interactions among 5900 proteins from >80 organisms; the vast majority from yeast, Helicobacter pylori and human. Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein-protein interactions available in the DIP database.
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            The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

            Henning Hermjakob, Luisa Montecchi-Palazzi, Gary Bader … (2004)
            A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).
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              The Biomolecular Interaction Network Database and related tools 2005 update

              C Alfarano, C. Andrade, K K Anthony … (2004)
              The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues.
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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 (pmc): nar
                Journal ID (publisher-id): Nucleic Acids Research
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): January 2007
                Publication date (Electronic): 29 November 2006
                Publication date PMC-release: 29 November 2006
                Volume: 35
                Issue: Database issue
                Pages: D557-D560
                Affiliations
                Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
                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
                DOI: 10.1093/nar/gkl961
                PMC ID: 1751533
                PubMed ID: 17135199
                SO-VID: de5013d1-e755-423f-ae6e-84c6269813e5
                Copyright © © 2006 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 : 08 August 2006
                Date revision received : 25 October 2006
                Date accepted : 25 October 2006
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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