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...
- Autores:
- 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
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- restrictedAccess
- License
- http://creativecommons.org/licenses/by-nc-nd/4.0/
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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. |
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2015 |
| dc.date.issued.none.fl_str_mv |
2015 |
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2020-03-26T16:32:46Z |
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2020-03-26T16:32:46Z |
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http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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http://purl.org/coar/resource_type/c_2df8fbb1 |
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info:eu-repo/semantics/article |
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info:eu-repo/semantics/publishedVersion |
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Artículo |
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publishedVersion |
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Current Bioinformatics; Vol. 10, Núm. 5; pp. 533-564 |
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15748936 |
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https://hdl.handle.net/20.500.12585/9011 |
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10.2174/1574893610666151008011457 |
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Universidad Tecnológica de Bolívar |
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Repositorio UTB |
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55665599200 56189852800 55363486500 56191215400 24436944800 55364135900 6506139148 6602882448 36454896800 |
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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 |
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https://hdl.handle.net/20.500.12585/9011 |
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eng |
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eng |
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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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