AN INNOVATIVE PROTOCOL FOR COMPARING PROTEIN BINDING SITES VIA ATOMIC GRID MAPS

M. Bicego, A. D. Favia, P. Bisignano, A. Cavalli, V. Murino

Abstract

This paper deals with a novel computational approach that aims to measure the similarities of protein binding sites through comparison of atomic grid maps. The assessment of structural similarity between proteins is a longstanding goal in biology and in structure-based drug design. Instead of focusing on standard structural alignment techniques, mostly based on superposition of common structural elements, the proposed approach starts from a physicochemical description of the proteins’ binding site. We call these atomic grid maps. These maps are preprocessed to reduce the dimensionality of the data while retaining the relevant information. Then, we devise an alignment-based similarity measure, based on a rigid registration algorithm (the Iterative Closest Point –ICP). The proposed approach, tested on a real dataset involving 22 proteins, has shown encouraging results in comparison with standard procedures.

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Paper Citation


in Harvard Style

Bicego M., D. Favia A., Bisignano P., Cavalli A. and Murino V. (2011). AN INNOVATIVE PROTOCOL FOR COMPARING PROTEIN BINDING SITES VIA ATOMIC GRID MAPS . In Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2011) ISBN 978-989-8425-79-9, pages 405-414. DOI: 10.5220/0003637404130422


in Bibtex Style

@conference{kdir11,
author={M. Bicego and A. D. Favia and P. Bisignano and A. Cavalli and V. Murino},
title={AN INNOVATIVE PROTOCOL FOR COMPARING PROTEIN BINDING SITES VIA ATOMIC GRID MAPS},
booktitle={Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2011)},
year={2011},
pages={405-414},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003637404130422},
isbn={978-989-8425-79-9},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2011)
TI - AN INNOVATIVE PROTOCOL FOR COMPARING PROTEIN BINDING SITES VIA ATOMIC GRID MAPS
SN - 978-989-8425-79-9
AU - Bicego M.
AU - D. Favia A.
AU - Bisignano P.
AU - Cavalli A.
AU - Murino V.
PY - 2011
SP - 405
EP - 414
DO - 10.5220/0003637404130422