Author, as appears in the article.: Garcia-Hernandez, Carlos; Fernandez, Alberto; Serratosa, Francesc
Department: Enginyeria Informàtica i Matemàtiques Enginyeria Química
URV's Author/s: Fernández Sabater, Alberto / Serratosa Casanelles, Francesc d'Assís
Project code: Grant agreement No. 713679
Keywords: Virtual screening Structure-activity relationships Molecular similarity Machine learning Ligands Learning Graph edit distance Extended reduced graph Drug evaluation, preclinical Databases, factual Computer graphics structure-activity relationships molecular similarity machine learning graph edit distance extended reduced graph
Abstract: Graph edit distance is a methodology used to solve error-tolerant graph matching. This methodology estimates a distance between two graphs by determining the minimum number of modifications required to transform one graph into the other. These modifications, known as edit operations, have an edit cost associated that has to be determined depending on the problem.This study focuses on the use of optimization techniques in order to learn the edit costs used when comparing graphs by means of the graph edit distance.Graphs represent reduced structural representations of molecules using pharmacophore-type node descriptions to encode the relevant molecular properties. This reduction technique is known as extended reduced graphs. The screening and statistical tools available on the ligand-based virtual screening benchmarking platform and the RDKit were used.In the experiments, the graph edit distance using learned costs performed better or equally good than using predefined costs. This is exemplified with six publicly available datasets: DUD-E, MUV, GLL&GDD, CAPST, NRLiSt BDB, and ULS-UDS.This study shows that the graph edit distance along with learned edit costs is useful to identify bioactivity similarities in a structurally diverse group of molecules. Furthermore, the target-specific edit costs might provide useful structure-activity information for future drug-design efforts.Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.
Thematic Areas: Saúde coletiva Química Psicología Planejamento urbano e regional / demografia Odontología Medicine (miscellaneous) Medicina iii Medicina ii Medicina i Interdisciplinar General medicine Farmacia Ensino Educação física Drug discovery Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências ambientais Chemistry, medicinal Biotecnología Biodiversidade Astronomia / física
Author's mail: alberto.fernandez@urv.cat francesc.serratosa@urv.cat
Author identifier: 0000-0002-1241-1646 0000-0001-6112-5913
Record's date: 2024-10-12
Papper version: info:eu-repo/semantics/publishedVersion
Link to the original source: https://www.eurekaselect.com/182468/article
Funding program: : Marie Skłodowska-Curie Actions - European Union's Horizon 2020 research and innovation programme
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Papper original source: Current Topics In Medicinal Chemistry. 20 (18): 1582-1592
APA: Garcia-Hernandez, Carlos; Fernandez, Alberto; Serratosa, Francesc (2020). Learning the Edit Costs of Graph Edit Distance Applied to Ligand-Based Virtual Screening. Current Topics In Medicinal Chemistry, 20(18), 1582-1592. DOI: 10.2174/1568026620666200603122000
Acronym: MFP
Article's DOI: 10.2174/1568026620666200603122000
Entity: Universitat Rovira i Virgili
Journal publication year: 2020
Funding program action: Martí i Franquès COFUND Doctoral Programme
Publication Type: Journal Publications