Author, as appears in the article.: Garcia-Hernandez C, Fernández A, Serratosa F

Department: Enginyeria Informàtica i Matemàtiques Enginyeria Química

URV's Author/s: Fernández Sabater, Alberto / GARCIA HERNANDEZ, CARLOS JESÚS / Serratosa Casanelles, Francesc d'Assís

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

Abstract: 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.

Thematic Areas: 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

licence for use: thttps://creativecommons.org/licenses/by/3.0/es/

ISSN: 15499596

Author's mail: francesc.serratosa@urv.cat alberto.fernandez@urv.cat

Author identifier: 0000-0001-6112-5913 0000-0002-1241-1646

Last page: 1421

Record's date: 2023-02-18

Journal volume: 59

Papper version: info:eu-repo/semantics/publishedVersion

Link to the original source: https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00820#

Licence document URL: http://repositori.urv.cat/ca/proteccio-de-dades/

Papper original source: Journal Of Chemical Information And Modeling. 59 (4): 1410-1421

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

Article's DOI: 10.1021/acs.jcim.8b00820

Entity: Universitat Rovira i Virgili

Journal publication year: 2019

First page: 1410

Publication Type: Journal Publications