TarO: a target optimisation system for structural biology

Ian M. Overton*, C. A. Johannes van Niekerk, Lester G. Carter, Alice Dawson, David M.A. Martin, Scott Cameron, Stephen A. McMahon, Malcolm F. White, William N. Hunter, James H. Naismith, Geoffrey J. Barton

*Corresponding author for this work

    Research output: Contribution to journalArticle

    31 Citations (Scopus)
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    Abstract

    TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC 'Structural Proteomics of Rational Targets' initiative.

    Original languageEnglish
    Pages (from-to)W190–W196
    Number of pages7
    JournalNucleic Acids Research
    Volume36
    Issue numberSuppl. 2
    Early online date3 Apr 2008
    DOIs
    Publication statusPublished - 1 Jul 2008

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    Colocasia
    Systems Biology
    Sequence Alignment
    Databases
    Computing Methodologies
    Management Information Systems
    Computer Communication Networks
    Post Translational Protein Processing
    Crystallization
    Computational Biology
    Proteomics
    Proteins

    Cite this

    Overton, I. M., van Niekerk, C. A. J., Carter, L. G., Dawson, A., Martin, D. M. A., Cameron, S., ... Barton, G. J. (2008). TarO: a target optimisation system for structural biology. Nucleic Acids Research, 36(Suppl. 2), W190–W196. https://doi.org/10.1093/nar/gkn141
    Overton, Ian M. ; van Niekerk, C. A. Johannes ; Carter, Lester G. ; Dawson, Alice ; Martin, David M.A. ; Cameron, Scott ; McMahon, Stephen A. ; White, Malcolm F. ; Hunter, William N. ; Naismith, James H. ; Barton, Geoffrey J. / TarO : a target optimisation system for structural biology. In: Nucleic Acids Research. 2008 ; Vol. 36, No. Suppl. 2. pp. W190–W196.
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    Overton, IM, van Niekerk, CAJ, Carter, LG, Dawson, A, Martin, DMA, Cameron, S, McMahon, SA, White, MF, Hunter, WN, Naismith, JH & Barton, GJ 2008, 'TarO: a target optimisation system for structural biology', Nucleic Acids Research, vol. 36, no. Suppl. 2, pp. W190–W196. https://doi.org/10.1093/nar/gkn141

    TarO : a target optimisation system for structural biology. / Overton, Ian M.; van Niekerk, C. A. Johannes; Carter, Lester G.; Dawson, Alice; Martin, David M.A.; Cameron, Scott; McMahon, Stephen A.; White, Malcolm F.; Hunter, William N.; Naismith, James H.; Barton, Geoffrey J.

    In: Nucleic Acids Research, Vol. 36, No. Suppl. 2, 01.07.2008, p. W190–W196.

    Research output: Contribution to journalArticle

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    T2 - a target optimisation system for structural biology

    AU - Overton, Ian M.

    AU - van Niekerk, C. A. Johannes

    AU - Carter, Lester G.

    AU - Dawson, Alice

    AU - Martin, David M.A.

    AU - Cameron, Scott

    AU - McMahon, Stephen A.

    AU - White, Malcolm F.

    AU - Hunter, William N.

    AU - Naismith, James H.

    AU - Barton, Geoffrey J.

    PY - 2008/7/1

    Y1 - 2008/7/1

    N2 - TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC 'Structural Proteomics of Rational Targets' initiative.

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    M3 - Article

    C2 - 18385152

    AN - SCOPUS:48449093586

    VL - 36

    SP - W190–W196

    JO - Nucleic Acids Research

    JF - Nucleic Acids Research

    SN - 0305-1048

    IS - Suppl. 2

    ER -

    Overton IM, van Niekerk CAJ, Carter LG, Dawson A, Martin DMA, Cameron S et al. TarO: a target optimisation system for structural biology. Nucleic Acids Research. 2008 Jul 1;36(Suppl. 2):W190–W196. https://doi.org/10.1093/nar/gkn141