Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?

The present manuscript describes a novel 3D-QSAR alignment free method (QuBiLS-MIDAS Duplex) based on algebraic bilinear, quadratic and linear forms on the kth two-tuple spatial-(dis)similarity matrix. Generalization schemes for the inter-atomic spatial distance using diverse (dis)-similarity measur...

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Tipo de recurso:
Fecha de publicación:
2015
Institución:
Universidad Tecnológica de Bolívar
Repositorio:
Repositorio Institucional UTB
Idioma:
eng
OAI Identifier:
oai:repositorio.utb.edu.co:20.500.12585/9011
Acceso en línea:
https://hdl.handle.net/20.500.12585/9011
Palabra clave:
3D-QSAR
Aggregation operator
Alignment free method
Minkowski distance matrix
Principal component analysis
QuBiLS-MIDAS
TOMOCOMD-CARDD
Two-tuple spatial-(dis)similarity matrix
Variability analysis
Corticosteroid
Globulin
Steroid
Article
Atom
Binding affinity
Data base
High throughput screening
Information
Methodology
Priority journal
Quantitative structure activity relation
Training
Rights
restrictedAccess
License
http://creativecommons.org/licenses/by-nc-nd/4.0/
id UTB2_9577d9ec05955e486c8fec2cad83383f
oai_identifier_str oai:repositorio.utb.edu.co:20.500.12585/9011
network_acronym_str UTB2
network_name_str Repositorio Institucional UTB
repository_id_str
dc.title.none.fl_str_mv Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?
title Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?
spellingShingle Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?
3D-QSAR
Aggregation operator
Alignment free method
Minkowski distance matrix
Principal component analysis
QuBiLS-MIDAS
TOMOCOMD-CARDD
Two-tuple spatial-(dis)similarity matrix
Variability analysis
Corticosteroid
Globulin
Steroid
Article
Atom
Binding affinity
Data base
High throughput screening
Information
Methodology
Priority journal
Quantitative structure activity relation
Training
title_short Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?
title_full Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?
title_fullStr Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?
title_full_unstemmed Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?
title_sort Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?
dc.subject.keywords.none.fl_str_mv 3D-QSAR
Aggregation operator
Alignment free method
Minkowski distance matrix
Principal component analysis
QuBiLS-MIDAS
TOMOCOMD-CARDD
Two-tuple spatial-(dis)similarity matrix
Variability analysis
Corticosteroid
Globulin
Steroid
Article
Atom
Binding affinity
Data base
High throughput screening
Information
Methodology
Priority journal
Quantitative structure activity relation
Training
topic 3D-QSAR
Aggregation operator
Alignment free method
Minkowski distance matrix
Principal component analysis
QuBiLS-MIDAS
TOMOCOMD-CARDD
Two-tuple spatial-(dis)similarity matrix
Variability analysis
Corticosteroid
Globulin
Steroid
Article
Atom
Binding affinity
Data base
High throughput screening
Information
Methodology
Priority journal
Quantitative structure activity relation
Training
description The present manuscript describes a novel 3D-QSAR alignment free method (QuBiLS-MIDAS Duplex) based on algebraic bilinear, quadratic and linear forms on the kth two-tuple spatial-(dis)similarity matrix. Generalization schemes for the inter-atomic spatial distance using diverse (dis)-similarity measures are discussed. On the other hand, normalization approaches for the two-tuple spatial-(dis)similarity matrix by using simple-and double-stochastic and mutual probability schemes are introduced. With the aim of taking into consideration particular inter-atomic interactions in total or local-fragment indices, path and length cut-off constraints are used. Also, in order to generalize the use of the linear combination of atom-level indices to yield global (molecular) definitions, a set of aggregation operators (invariants) are applied. A Shannon’s entropy based variability study for the proposed 3D algebraic form-based indices and the DRAGON molecular descriptor families demonstrates superior performance for the former. A principal component analysis reveals that the novel indices codify structural information orthogonal to those captured by the DRAGON indices. Finally, a QSAR study for the binding affinity to the corticosteroid-binding globulin using Cramer’s steroid database is performed. From this study, it is revealed that the QuBiLS-MIDAS Duplex approach yields similar-to-superior performance statistics than all the 3D-QSAR methods reported in the literature reported so far, even with lower degree of freedom, using both the 31 steroids as the training set and the popular division of Cramer’s database in training [1-21] and test sets [22-31]. It is thus expected that this methodology provides useful tools for the diversity analysis of compound datasets and high-throughput screening structure–activity data. © 2015 Bentham Science Publishers.
publishDate 2015
dc.date.issued.none.fl_str_mv 2015
dc.date.accessioned.none.fl_str_mv 2020-03-26T16:32:46Z
dc.date.available.none.fl_str_mv 2020-03-26T16:32:46Z
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dc.type.driver.none.fl_str_mv info:eu-repo/semantics/article
dc.type.hasversion.none.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.spa.none.fl_str_mv Artículo
status_str publishedVersion
dc.identifier.citation.none.fl_str_mv Current Bioinformatics; Vol. 10, Núm. 5; pp. 533-564
dc.identifier.issn.none.fl_str_mv 15748936
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12585/9011
dc.identifier.doi.none.fl_str_mv 10.2174/1574893610666151008011457
dc.identifier.instname.none.fl_str_mv Universidad Tecnológica de Bolívar
dc.identifier.reponame.none.fl_str_mv Repositorio UTB
dc.identifier.orcid.none.fl_str_mv 55665599200
56189852800
55363486500
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identifier_str_mv Current Bioinformatics; Vol. 10, Núm. 5; pp. 533-564
15748936
10.2174/1574893610666151008011457
Universidad Tecnológica de Bolívar
Repositorio UTB
55665599200
56189852800
55363486500
56191215400
24436944800
55364135900
6506139148
6602882448
36454896800
url https://hdl.handle.net/20.500.12585/9011
dc.language.iso.none.fl_str_mv eng
language eng
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_16ec
dc.rights.uri.none.fl_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.accessrights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
dc.rights.cc.none.fl_str_mv Atribución-NoComercial 4.0 Internacional
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
Atribución-NoComercial 4.0 Internacional
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dc.format.medium.none.fl_str_mv Recurso electrónico
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dc.publisher.none.fl_str_mv Bentham Science Publishers B.V.
publisher.none.fl_str_mv Bentham Science Publishers B.V.
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spelling 2020-03-26T16:32:46Z2020-03-26T16:32:46Z2015Current Bioinformatics; Vol. 10, Núm. 5; pp. 533-56415748936https://hdl.handle.net/20.500.12585/901110.2174/1574893610666151008011457Universidad Tecnológica de BolívarRepositorio UTB5566559920056189852800553634865005619121540024436944800553641359006506139148660288244836454896800The present manuscript describes a novel 3D-QSAR alignment free method (QuBiLS-MIDAS Duplex) based on algebraic bilinear, quadratic and linear forms on the kth two-tuple spatial-(dis)similarity matrix. Generalization schemes for the inter-atomic spatial distance using diverse (dis)-similarity measures are discussed. On the other hand, normalization approaches for the two-tuple spatial-(dis)similarity matrix by using simple-and double-stochastic and mutual probability schemes are introduced. With the aim of taking into consideration particular inter-atomic interactions in total or local-fragment indices, path and length cut-off constraints are used. Also, in order to generalize the use of the linear combination of atom-level indices to yield global (molecular) definitions, a set of aggregation operators (invariants) are applied. A Shannon’s entropy based variability study for the proposed 3D algebraic form-based indices and the DRAGON molecular descriptor families demonstrates superior performance for the former. A principal component analysis reveals that the novel indices codify structural information orthogonal to those captured by the DRAGON indices. Finally, a QSAR study for the binding affinity to the corticosteroid-binding globulin using Cramer’s steroid database is performed. From this study, it is revealed that the QuBiLS-MIDAS Duplex approach yields similar-to-superior performance statistics than all the 3D-QSAR methods reported in the literature reported so far, even with lower degree of freedom, using both the 31 steroids as the training set and the popular division of Cramer’s database in training [1-21] and test sets [22-31]. It is thus expected that this methodology provides useful tools for the diversity analysis of compound datasets and high-throughput screening structure–activity data. © 2015 Bentham Science Publishers.Recurso electrónicoapplication/pdfengBentham Science Publishers B.V.http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/restrictedAccessAtribución-NoComercial 4.0 Internacionalhttp://purl.org/coar/access_right/c_16echttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84927733368&doi=10.2174%2f1574893610666151008011457&partnerID=40&md5=49527a3c26afe0288f993e0ca3414432Optimum search strategies or novel 3D molecular descriptors: Is there a stalemate?info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_2df8fbb13D-QSARAggregation operatorAlignment free methodMinkowski distance matrixPrincipal component analysisQuBiLS-MIDASTOMOCOMD-CARDDTwo-tuple spatial-(dis)similarity matrixVariability analysisCorticosteroidGlobulinSteroidArticleAtomBinding affinityData baseHigh throughput screeningInformationMethodologyPriority journalQuantitative structure activity relationTrainingMarrero-Ponce Y.García-Jacas C.R.Barigye S.J.Valdés-Martiní J.R.Rivera-Borroto O.M.Pino-Urias R.W.Cubillán, NéstorAlvarado Y.J.Le-Thi-Thu H.Kubinyi, H., QSAR and 3D QSAR in Drug Design: 1. 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