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      Scalable web services for the PSIPRED Protein Analysis Workbench

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          Abstract

          Here, we present the new UCL Bioinformatics Group’s PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.

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          Most cited references17

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          Reorganizing the protein space at the Universal Protein Resource (UniProt)

          emmanuel boutet, Claire O'Donovan (2011)
          The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. A key development at UniProt is the provision of complete, reference and representative proteomes. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.
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            The RCSB Protein Data Bank: new resources for research and education

            Peter W Rose, Chunxiao Bi, Wolfgang Bluhm … (2012)
            The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher’s PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.
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              Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.

              S F Altschul, E. V. Koonin (1998)
              Article 0 comments Cited 177 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 (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 (Print): July 2013
                Publication date (Electronic): 8 June 2013
                Publication date PMC-release: 8 June 2013
                Volume: 41
                Issue: Web Server issue
                Pages: W349-W357
                Affiliations
                Department of Computer Science, University College London, Gower Street, London, WC1E 6BT
                Author notes
                *To whom correspondence should be addressed. Tel: +44 20 76793718; Fax: +44 20 73871397; Email: d.buchan@ 123456cs.ucl.ac.uk
                Correspondence may also be addressed to David T. Jones. Tel: +44 20 7679 7982; Fax: +44 20 7387 1397; Email: d.t.jones@ 123456ucl.ac.uk
                Article
                Publisher ID: gkt381
                DOI: 10.1093/nar/gkt381
                PMC ID: 3692098
                PubMed ID: 23748958
                SO-VID: de8bf31c-7648-4ce8-bc2a-157af22012c9
                Copyright © © The Author(s) 2013. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 31 January 2013
                Date revision received : 12 April 2013
                Date accepted : 18 April 2013
                Page count
                Pages: 9
                Categories
                Subject: Articles
                Custom metadata
                cover-date 1 July 2013

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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