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Bioinformatics Advance Access originally published online on February 25, 2009
Bioinformatics 2009 25(9):1201-1202; doi:10.1093/bioinformatics/btp111
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes

Timothy V. Pyrkov 1,2,*, Anton O. Chugunov 1, Nikolay A. Krylov 1,2, Dmitry E. Nolde 1 and Roman G. Efremov 1

1M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 GSP, Moscow V-437 and 2Moscow Institute of Physics and Technology (State University), 141700, Institutskii per., 9, Dolgoprudny, Moscow region, Russia

*To whom correspondence should be addressed.


  Abstract

Summary: The PLATINUM (Protein–Ligand ATtractions Investigation NUMerically) web service is designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative characterization of the hydrophobic/hydrophilic match in biomolecular complexes e.g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical Molecular Hydrophobicity Potential (MHP).

Availability: The PLATINUM web tool as well as detailed documentation and tutorial are available free of charge for academic users at http://model.nmr.ru/platinum/. PLATINUM requires Java 5 or higher and Adobe Flash Player 9.

Contact: pyrkov{at}nmr.ru

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on November 27, 2008; revised on February 4, 2009; accepted on February 22, 2009

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