Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields

Descriptors based on Molecular Interaction Fields (MIF) are highly suitable for drug discovery, but their size (thousands of variables) often limits their application in practice. Here we describe a simple and fast computational method that extracts from a MIF a handful of highly informative points...

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Detalhes bibliográficos
Autores: Durán Alcaide, Ángel, Martínez, Guillermo C., Pastor Maeso, Manuel
Tipo de documento: artigo
Estado:Versión enviada para evaluación y publicación
Data de publicação:2008
País:España
Recursos:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositório:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/16647
Acesso em linha:http://hdl.handle.net/10230/16647
http://dx.doi.org/10.1021/ci800037t
Access Level:Acceso aberto
Palavra-chave:Molècules -- Models -- Simulació per ordinador
Medicaments -- Disseny -- Simulació per ordinador
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spelling Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction FieldsDurán Alcaide, ÁngelMartínez, Guillermo C.Pastor Maeso, ManuelMolècules -- Models -- Simulació per ordinadorMedicaments -- Disseny -- Simulació per ordinadorDescriptors based on Molecular Interaction Fields (MIF) are highly suitable for drug discovery, but their size (thousands of variables) often limits their application in practice. Here we describe a simple and fast computational method that extracts from a MIF a handful of highly informative points (hot spots) which summarize the most relevant information. The method was specifically developed for drug discovery, is fast, and does not require human supervision, being suitable for its application on very large series of compounds. The quality of the results has been tested by running the method on the ligand structure of a large number of ligand-receptor complexes and then comparing the position of the selected hot spots with actual atoms of the receptor. As an additional test, the hot spots obtained with the novel method were used to obtain GRIND-like molecular descriptors which were compared with the original GRIND. In both cases the results show that the novel method is highly suitable for describing ligand-receptor interactions and compares favorably with other state-of-the-art methods.American Chemical Society (ACS)201220122008info:eu-repo/semantics/articleinfo:eu-repo/semantics/submittedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/16647http://dx.doi.org/10.1021/ci800037treponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésJournal of Chemical Information and Modeling. 2008;48(9):1813-23© 2008, American Chemical Society (ACS). This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of Chemical Information and Modeling, copyright © American Chemical Society after peer review. To access the final edited and published work see http://pubs.acs.org/doi/abs/10.1021/ci800037tinfo:eu-repo/semantics/openAccessoai:recercat.cat:10230/166472026-05-29T05:05:01Z
dc.title.none.fl_str_mv Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields
title Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields
spellingShingle Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields
Durán Alcaide, Ángel
Molècules -- Models -- Simulació per ordinador
Medicaments -- Disseny -- Simulació per ordinador
title_short Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields
title_full Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields
title_fullStr Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields
title_full_unstemmed Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields
title_sort Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields
dc.creator.none.fl_str_mv Durán Alcaide, Ángel
Martínez, Guillermo C.
Pastor Maeso, Manuel
author Durán Alcaide, Ángel
author_facet Durán Alcaide, Ángel
Martínez, Guillermo C.
Pastor Maeso, Manuel
author_role author
author2 Martínez, Guillermo C.
Pastor Maeso, Manuel
author2_role author
author
dc.subject.none.fl_str_mv Molècules -- Models -- Simulació per ordinador
Medicaments -- Disseny -- Simulació per ordinador
topic Molècules -- Models -- Simulació per ordinador
Medicaments -- Disseny -- Simulació per ordinador
description Descriptors based on Molecular Interaction Fields (MIF) are highly suitable for drug discovery, but their size (thousands of variables) often limits their application in practice. Here we describe a simple and fast computational method that extracts from a MIF a handful of highly informative points (hot spots) which summarize the most relevant information. The method was specifically developed for drug discovery, is fast, and does not require human supervision, being suitable for its application on very large series of compounds. The quality of the results has been tested by running the method on the ligand structure of a large number of ligand-receptor complexes and then comparing the position of the selected hot spots with actual atoms of the receptor. As an additional test, the hot spots obtained with the novel method were used to obtain GRIND-like molecular descriptors which were compared with the original GRIND. In both cases the results show that the novel method is highly suitable for describing ligand-receptor interactions and compares favorably with other state-of-the-art methods.
publishDate 2008
dc.date.none.fl_str_mv 2008
2012
2012
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/submittedVersion
format article
status_str submittedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/16647
http://dx.doi.org/10.1021/ci800037t
url http://hdl.handle.net/10230/16647
http://dx.doi.org/10.1021/ci800037t
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Journal of Chemical Information and Modeling. 2008;48(9):1813-23
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Chemical Society (ACS)
publisher.none.fl_str_mv American Chemical Society (ACS)
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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