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      The PMDB Protein Model Database

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ∼240 proteins. The system is accessible at http://www.caspur.it/PMDB and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data.

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          VERIFY3D: assessment of protein models with three-dimensional profiles.

          D Eisenberg, R Lüthy, J U Bowie (1997)
          Article 0 comments Cited 365 times – based on 0 reviews     Review now
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            RASMOL: biomolecular graphics for all

            R Sayle (1995)
            Article 0 comments Cited 354 times – based on 0 reviews     Review now
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              Database resources of the National Center for Biotechnology Information

              David Wheeler, Tanya Barrett, Dennis A Benson … (2004)
              In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data retrieval systems and computational resources for the analysis of data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, Entrez Programming Utilities, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.
              Article 0 comments Cited 157 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                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 Collection: 01 January 2006
                Publication date (Print): 01 January 2006
                Publication date (Electronic): 28 December 2005
                Volume: 34
                Issue: Database issue
                Pages: D306-D309
                Affiliations
                CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca Via dei Tizii, 6/b, I-00185 Rome, Italy
                1Department of Biochemical Sciences, University ‘La Sapienza’ P.le Aldo Moro, 5, I-00185 Rome, Italy
                2Istituto Pasteur—Fondazione Cenci Bolognetti, University ‘La Sapienza’ P.le Aldo Moro, 5, I-00185 Rome, Italy
                Author notes
                *To whom correspondence should be addressed. Tel: +39 0649910556; Fax: +39 0649910717; Email: anna.tramontano@ 123456uniroma1.it
                Article
                DOI: 10.1093/nar/gkj105
                PMC ID: 1347467
                PubMed ID: 16381873
                SO-VID: 48ef26a3-4d27-46ae-a2be-85dbd24fb3dc
                Copyright © © The Author 2006. Published by Oxford University Press. All rights reserved
                License:

                The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@ 123456oxfordjournals.org

                History
                Date received : 28 July 2005
                Date revision received : 17 October 2005
                Date accepted : 17 October 2005
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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