GEOMETRICAL CONSTRAINTS FOR LIGAND POSITIONING

Virginio Cantoni; Alessandro Gaggia; Riccardo Gatti; Luca Lombardi

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Paper

GEOMETRICAL CONSTRAINTS FOR LIGAND POSITIONING

Topics: Genomics and Proteomics; Pattern Recognition, Clustering and Classification

In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 0BIOSTEC, 204-209, 2011 , Rome, Italy

Authors: Virginio Cantoni ; Alessandro Gaggia ; Riccardo Gatti and Luca Lombardi

Affiliation: University of Pavia, Italy

Keyword(s): Protein-ligand interaction, active sites detection, Extended Gaussian Image, alignment of biological molecules, structural matching, mathematical morphology

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Pattern Recognition, Clustering and Classification

Abstract: The purpose of the activity here described is the morphological and subsequently the geometrical and topological analysis of the active sites in protein surfaces for protein-ligand docking. The approach follows a sequence of three steps: i) the solvent-excluded-surface is analyzed and segmented in a number of pockets and tunnels; ii) the candidate binding sites are detected through a structural matching of pockets and ligand, both represented through a suitable Extended Gaussian Image modality; iii) the loci of compatible positions of the ligand is identified through mathematical morphology. This representation of ligand and candidate binding pockets, the comparison of the morphological similarity and the identification of potential ligand docking are the novelties of this proposal.

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Paper citation in several formats:

Cantoni, V.; Gaggia, A.; Gatti, R. and Lombardi, L. (2011). GEOMETRICAL CONSTRAINTS FOR LIGAND POSITIONING. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS; ISBN 978-989-8425-36-2; ISSN 2184-4305, SciTePress, pages 204-209. DOI: 10.5220/0003166002040209

@conference{bioinformatics11,
author={Virginio Cantoni. and Alessandro Gaggia. and Riccardo Gatti. and Luca Lombardi.},
title={GEOMETRICAL CONSTRAINTS FOR LIGAND POSITIONING},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS},
year={2011},
pages={204-209},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003166002040209},
isbn={978-989-8425-36-2},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS
TI - GEOMETRICAL CONSTRAINTS FOR LIGAND POSITIONING
SN - 978-989-8425-36-2
IS - 2184-4305
AU - Cantoni, V.
AU - Gaggia, A.
AU - Gatti, R.
AU - Lombardi, L.
PY - 2011
SP - 204
EP - 209
DO - 10.5220/0003166002040209
PB - SciTePress