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Authors: Virginio Cantoni ; Riccardo Gatti and Luca Lombardi

Affiliation: University of Pavia, Italy

ISBN: 978-989-674-019-1

Keyword(s): Protein-ligand docking, Curvature analysis, Concavity tree, Travel depth, Pocket mouth area and perimeter.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Structural Bioinformatics

Abstract: The development of computational techniques to guide the experimental processes is an important step for the determination of the protein functions. The purpose of the activity here described is the characterization of the active sites in protein surfaces and their quantitative representation. A few pocket parameters like volume, travel depth, mouth area and perimeter, amplitude parameters, interfacial area ratio, summit density and mean summit curvature are hierarchically accessible through a concavity tree that topologically represents the entire protein molecule. This structural representation is particularly useful for the evaluation of binding pockets, the comparison of the morphological similarity and the identification of potential ligand docking.

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Paper citation in several formats:
Cantoni V.; Gatti R.; Lombardi L. and (2010). PROTEINS POCKETS ANALYSIS AND DESCRIPTION.In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 211-216. DOI: 10.5220/0002725302110216

@conference{bioinformatics10,
author={Virginio Cantoni and Riccardo Gatti and Luca Lombardi},
title={PROTEINS POCKETS ANALYSIS AND DESCRIPTION},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={211-216},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002725302110216},
isbn={978-989-674-019-1},
}

TY - CONF

JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - PROTEINS POCKETS ANALYSIS AND DESCRIPTION
SN - 978-989-674-019-1
AU - Cantoni, V.
AU - Gatti, R.
AU - Lombardi, L.
PY - 2010
SP - 211
EP - 216
DO - 10.5220/0002725302110216

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