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

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• 作者：Néstor Cubillán ; Yovani Marrero-Ponce…
• 关键词：TOMOCOMD ; CARDD ; 3D ; linear index ; Variability analysis ; QSPR study
• 刊名：Journal of Mathematical Chemistry
• 出版年：2015
• 出版时间：October 2015
• 年：2015
• 卷：53
• 期：9
• 页码：2028-2064
• 全文大小：1,352 KB
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• 作者单位：Néstor Cubillán (1) (2)
  Yovani Marrero-Ponce (3) (4)
  Harold Ariza-Rico (1)
  Stephen J. Barigye (5)
  César R. García-Jacas (6)
  José R. Valdes-Martini (7)
  Ysaías J. Alvarado (8)
  
  1. Laboratorio de Electrónica Molecular, Departamento de Química, Facultad Experimental de Ciencias, Universidad del Zulia, Maracaibo, Bolivarian Republic of Venezuela
  2. Departamento de Física, Facultad Experimental de Ciencias, Centro de Modelado Científico, Universidad del Zulia, Maracaibo, Bolivarian Republic of Venezuela
  3. Computer-Aided Molecular “Biosilico-Discovery and Bioinformatic Research International Network (CAMD-BIR IN), Los Laureles L76MD, Nuevo Bosque, 130015, Cartagena de Indias, Bolívar, Colombia
  4. Grupo de Investigación en Estudios Químicos y Biológicos, Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar (UTB), Parque Industrial y Tecnológico Carlos Vélez Pombo, Km 1 vía Turbaco, 130010, Cartagena de Indias, Bolívar, Colombia
  5. Departamento de Química, Universidade Federal de Lavras, Lavras, MG, Brazil
  6. Departamento de Bioinformática, Universidad de las Ciencias Informáticas, Havana, Cuba
  7. Laboratorio de Inteligencia Artificial, Facultad de Matemática, Física y Computación, Centro de Estudios de Informática (CEI), Universidad Central “Marta Abreu-de Las Villas, Santa Clara, 54830, Villa Clara, Cuba
  8. Laboratorio de Caracterización Molecular y Biomolecular, Departamento de Investigación en Tecnología de los Materiales y el Ambiente (DITeMA), Instituto Venezolano de Investigaciones Científicas (IVIC), Avenida 74 con calle 14A, Maracaibo, Bolivarian Republic of Venezuela
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Physical Chemistry
  Theoretical and Computational Chemistry
  Mathematical Applications in Chemistry
  
• 出版者：Springer Netherlands
• ISSN：1572-8897

文摘

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. Keywords TOMOCOMD-CARDD 3D-linear index Variability analysis QSPR study