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Bioinformatics 2007 23(2):e104-e109; doi:10.1093/bioinformatics/btl292
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Computer Aided Drug Design

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family

Rafael J. Najmanovich 1,2,*, Abdellah Allali-Hassani 2, Richard J. Morris 1,{dagger}, Ludmila Dombrovsky 2, Patricia W. Pan 3, Masoud Vedadi 2, Alexander N. Plotnikov 2,4, Aled Edwards 2,5, Cheryl Arrowsmith 2,5 and Janet M. Thornton 1

1 European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus Cambridge CB10 1SD, UK
2 Structural Genomics Consortium, University of Toronto Toronto, Ontario, Canada M5G 1L6
3 Department of Medical Biophysics, University of Toronto Toronto, Ontario, Canada M5G 1L6
4 Physiology Department, University of Toronto Toronto, Ontario, Canada M5G 1L6
5 Banting and Best Department of Medical Research, University of Toronto Toronto, Ontario, Canada M5G 1L6

*To whom correspondence should be addressed.


  Abstract

Motivation: In the present work we combine computational analysis and experimental data to explore the extent to which binding site similarities between members of the human cytosolic sulfotransferase family correlate with small-molecule binding profiles. Conversely, from a small-molecule point of view, we explore the extent to which structural similarities between small molecules correlate to protein binding profiles.

Results: The comparison of binding site structural similarities and small-molecule binding profiles shows that proteins with similar small-molecule binding profiles tend to have a higher degree of binding site similarity but the latter is not sufficient to predict small-molecule binding patterns, highlighting the difficulty of predicting small-molecule binding patterns from sequence or structure. Likewise, from a small-molecule perspective, small molecules with similar protein binding profiles tend to be topologically similar but topological similarity is not sufficient to predict their protein binding patterns. These observations have important consequences for function prediction and drug design.

Contact: rafael.najmanovich{at}ebi.ac.uk

{dagger}Present address: John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK


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