Autor según el artículo: Garcia-Hernandez C, Fernández A, Serratosa F

Departamento: Enginyeria Informàtica i Matemàtiques Enginyeria Química

Autor/es de la URV: Fernández Sabater, Alberto / GARCIA HERNANDEZ, CARLOS JESÚS / Serratosa Casanelles, Francesc d'Assís

Palabras clave: Validation Sets Metrics Diversity analysis Design Descriptor Chemistry Chemical-structures

Resumen: Copyright © 2019 American Chemical Society. Extended reduced graphs provide summary representations of chemical structures using pharmacophore-type node descriptions to encode the relevant molecular properties. Commonly used similarity measures using reduced graphs convert these graphs into 2D vectors like fingerprints, before chemical comparisons are made. This study investigates the effectiveness of a graph-only driven molecular comparison by using extended reduced graphs along with graph edit distance methods for molecular similarity calculation as a tool for ligand-based virtual screening applications, which estimate the bioactivity of a chemical on the basis of the bioactivity of similar compounds. The results proved to be very stable and the graph editing distance method performed better than other methods previously used on reduced graphs. This is exemplified with six publicly available data sets: DUD-E, MUV, GLL&GDD, CAPST, NRLiSt BDB, and ULS-UDS. The screening and statistical tools available on the ligand-based virtual screening benchmarking platform and the RDKit were also used. In the experiments, our method performed better than other molecular similarity methods which use array representations in most cases. Overall, it is shown that extended reduced graphs along with graph edit distance is a combination of methods that has numerous applications and can identify bioactivity similarities in a structurally diverse group of molecules.

Áreas temáticas: Química Medicina ii Medicina i Materiais Library and information sciences Interdisciplinar General chemistry General chemical engineering Farmacia Ensino Engenharias ii Computer science, interdisciplinary applications Computer science, information systems Computer science applications Ciencias sociales Ciências biológicas ii Ciências biológicas i Ciências ambientais Ciências agrárias i Ciência da computação Chemistry, multidisciplinary Chemistry, medicinal Chemistry (miscellaneous) Chemistry (all) Chemical engineering (miscellaneous) Chemical engineering (all) Biotecnología Astronomia / física

Acceso a la licencia de uso: thttps://creativecommons.org/licenses/by/3.0/es/

ISSN: 15499596

Direcció de correo del autor: francesc.serratosa@urv.cat alberto.fernandez@urv.cat

Identificador del autor: 0000-0001-6112-5913 0000-0002-1241-1646

Página final: 1421

Fecha de alta del registro: 2023-02-18

Volumen de revista: 59

Versión del articulo depositado: info:eu-repo/semantics/publishedVersion

Enlace a la fuente original: https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00820#

URL Documento de licencia: http://repositori.urv.cat/ca/proteccio-de-dades/

Referencia al articulo segun fuente origial: Journal Of Chemical Information And Modeling. 59 (4): 1410-1421

Referencia de l'ítem segons les normes APA: Garcia-Hernandez C, Fernández A, Serratosa F (2019). Ligand-based virtual screening using graph edit distance as molecular similarity measure. Journal Of Chemical Information And Modeling, 59(4), 1410-1421. DOI: 10.1021/acs.jcim.8b00820

DOI del artículo: 10.1021/acs.jcim.8b00820

Entidad: Universitat Rovira i Virgili

Año de publicación de la revista: 2019

Página inicial: 1410

Tipo de publicación: Journal Publications