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Bioinformatics Advance Access originally published online on May 5, 2006
Bioinformatics 2006 22(14):1702-1709; doi:10.1093/bioinformatics/btl178
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PROXIMO—a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS)

Sebastien K. Gerega and Kevin M. Downard *

School of Molecular and Microbial Biosciences, The University of Sydney Sydney, NSW 2006, Australia

*To whom correspondence should be addressed.

The design and implementation of a new algorithm, known as PROXIMO for protein oxidation interface modeller, is described to predict the structure of protein complexes using data generated in radical probe mass spectrometry (RP-MS) experiments. Photochemical radiolysis and discharge sources can be used to effect RP-MS in which hydroxyl radicals are formed directly from the bulk solvent on millisecond timescales and react with surface accessible residues in footprinting-like experiments. The algorithm utilizes a geometric surface fitting routine to predict likely structures for protein complexes. These structures are scored based on a correlation between the measured solvent accessibility of oxidizable residue side chains and oxidation shielding data obtained by RP-MS. The algorithm has been implemented to predict structures for the ribonuclease S-protein–peptide and calmodulin–melittin complexes using RP-MS data generated in this laboratory. The former is in close agreement with the high-resolution experimental structure available.

Contact: kdownard{at}usyd.edu.au

Received on February 28, 2006; revised on April 17, 2006; accepted on May 3, 2006

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