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Nucleic Acids Research Advance Access originally published online on April 2, 2008
Nucleic Acids Research 2008 36(Web Server issue):W190-W196; doi:10.1093/nar/gkn141
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W190-W196
© 2008 The Author(s)
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.

Articles

TarO: a target optimisation system for structural biology

Ian M. Overton1, C. A. Johannes van Niekerk1, Lester G. Carter2, Alice Dawson1, David M. A. Martin1, Scott Cameron1, Stephen A. McMahon2, Malcolm F. White2, William N. Hunter1, James H. Naismith2 and Geoffrey J. Barton1,*

1School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH and 2Centre for Biomolecular Sciences, School of Biomedical Science, North Haugh, The University, St Andrews, KY16 9ST, UK

*To whom correspondence should be addressed. Tel: +44 1382 385860; Fax: +44 1382 385764; Email: geoff{at}compbio.dundee.ac.uk

Received January 31, 2008. Revised March 13, 2008. Accepted March 16, 2008.

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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