Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications

A new family of alignment-free 3D descriptors based on TOMOCOMD-CARDD framework has been designed, namely 3D-linear indices. In this report, we have proposed the use of a generalized form of the geometric pairwise atom-atom distance matrix as structural information matrix. This matrix, denominated a...

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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:20.500.12585/9012
Acceso en línea:
https://hdl.handle.net/20.500.12585/9012
Palabra clave:
3D-linear index
QSPR study
TOMOCOMD-CARDD
Variability analysis
Rights
restrictedAccess
License
http://creativecommons.org/licenses/by-nc-nd/4.0/
id UTB2_a955d40694f6f673c6c3ccbc5b2c1f51
oai_identifier_str oai:repositorio.utb.edu.co:20.500.12585/9012
network_acronym_str UTB2
network_name_str Repositorio Institucional UTB
repository_id_str
dc.title.none.fl_str_mv Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications
title Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications
spellingShingle Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications
3D-linear index
QSPR study
TOMOCOMD-CARDD
Variability analysis
title_short Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications
title_full Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications
title_fullStr Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications
title_full_unstemmed Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications
title_sort Novel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applications
dc.subject.keywords.none.fl_str_mv 3D-linear index
QSPR study
TOMOCOMD-CARDD
Variability analysis
topic 3D-linear index
QSPR study
TOMOCOMD-CARDD
Variability analysis
description A new family of alignment-free 3D descriptors based on TOMOCOMD-CARDD framework has been designed, namely 3D-linear indices. In this report, we have proposed the use of a generalized form of the geometric pairwise atom-atom distance matrix as structural information matrix. This matrix, denominated as non-stochastic, uses as matrix form of linear maps as well as their algebraic transformations: stochastic, double stochastic and mutual probabilities matrices. The methodology for 3D-QSAR studies is based on the combined use of global and local approaches. Principal component analysis reveals that the novel indices are capable of capturing structural information not codified by the indices implemented in the DRAGON’s software. Moreover, Shannon’s entropy based variability analysis comparing the 3D-linear indices with some relevant descriptors suggests that the former encode similar-to-better amount of structural information than these descriptors. Finally, a search for the best regressions for congeneric databases in QSPR modeling was performed. The overall results demonstrates satisfactory behavior. © 2015, Springer International Publishing Switzerland.
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
dc.type.coarversion.fl_str_mv http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_2df8fbb1
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 Journal of Mathematical Chemistry; Vol. 53, Núm. 9; pp. 2028-2064
dc.identifier.issn.none.fl_str_mv 02599791
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12585/9012
dc.identifier.doi.none.fl_str_mv 10.1007/s10910-015-0533-3
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 6506139148
55665599200
56724217800
55363486500
56189852800
56191215400
6602882448
identifier_str_mv Journal of Mathematical Chemistry; Vol. 53, Núm. 9; pp. 2028-2064
02599791
10.1007/s10910-015-0533-3
Universidad Tecnológica de Bolívar
Repositorio UTB
6506139148
55665599200
56724217800
55363486500
56189852800
56191215400
6602882448
url https://hdl.handle.net/20.500.12585/9012
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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eu_rights_str_mv restrictedAccess
dc.format.medium.none.fl_str_mv Recurso electrónico
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Kluwer Academic Publishers
publisher.none.fl_str_mv Kluwer Academic Publishers
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institution Universidad Tecnológica de Bolívar
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spelling 2020-03-26T16:32:46Z2020-03-26T16:32:46Z2015Journal of Mathematical Chemistry; Vol. 53, Núm. 9; pp. 2028-206402599791https://hdl.handle.net/20.500.12585/901210.1007/s10910-015-0533-3Universidad Tecnológica de BolívarRepositorio UTB650613914855665599200567242178005536348650056189852800561912154006602882448A new family of alignment-free 3D descriptors based on TOMOCOMD-CARDD framework has been designed, namely 3D-linear indices. In this report, we have proposed the use of a generalized form of the geometric pairwise atom-atom distance matrix as structural information matrix. This matrix, denominated as non-stochastic, uses as matrix form of linear maps as well as their algebraic transformations: stochastic, double stochastic and mutual probabilities matrices. The methodology for 3D-QSAR studies is based on the combined use of global and local approaches. Principal component analysis reveals that the novel indices are capable of capturing structural information not codified by the indices implemented in the DRAGON’s software. Moreover, Shannon’s entropy based variability analysis comparing the 3D-linear indices with some relevant descriptors suggests that the former encode similar-to-better amount of structural information than these descriptors. Finally, a search for the best regressions for congeneric databases in QSPR modeling was performed. The overall results demonstrates satisfactory behavior. © 2015, Springer International Publishing Switzerland.Consejo de Desarrollo Científico, Humanístico y Tecnológico, Universidad del Zulia, CONDES: CC-0593-10 Ministerio de Ciencia e Innovación, MICINN: SAF2009-10399Recurso electrónicoapplication/pdfengKluwer Academic Publishershttp://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-s2.0-84940895558&doi=10.1007%2fs10910-015-0533-3&partnerID=40&md5=110f6f0a34ca458f52945b067ad8b9dbNovel global and local 3D atom-based linear descriptors of the Minkowski distance matrix: theory, diversity–variability analysis and QSPR applicationsinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_2df8fbb13D-linear indexQSPR studyTOMOCOMD-CARDDVariability analysisCubillán, NéstorMarrero-Ponce Y.Ariza-Rico H.Barigye S.J.García-Jacas C.R.Valdes-Martini J.R.Alvarado Y.J.Clark, D.E., Pickett, S.D., (2000) Drug Discov. 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Model., 20, p. 269. , COI: 1:CAS:528:DC%2BD3MXpt1art7o%3Dhttp://purl.org/coar/resource_type/c_6501THUMBNAILMiniProdInv.pngMiniProdInv.pngimage/png23941https://repositorio.utb.edu.co/bitstream/20.500.12585/9012/1/MiniProdInv.png0cb0f101a8d16897fb46fc914d3d7043MD5120.500.12585/9012oai:repositorio.utb.edu.co:20.500.12585/90122023-05-25 16:23:25.563Repositorio Institucional UTBrepositorioutb@utb.edu.co

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