Articles producció científica> Enginyeria Química

Learning the Edit Costs of Graph Edit Distance Applied to Ligand-Based Virtual Screening

  • Dades identificatives

    Identificador: imarina:8015488
    Autors:
    Garcia-Hernandez, CarlosFernandez, AlbertoSerratosa, Francesc
    Resum:
    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.
  • Altres:

    Autor segons l'article: Garcia-Hernandez, Carlos; Fernandez, Alberto; Serratosa, Francesc
    Departament: Enginyeria Informàtica i Matemàtiques Enginyeria Química
    Autor/s de la URV: Fernández Sabater, Alberto / Serratosa Casanelles, Francesc d'Assís
    Codi de projecte: Grant agreement No. 713679
    Paraules clau: 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
    Resum: 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.
    Àrees temàtiques: 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
    Adreça de correu electrònic de l'autor: alberto.fernandez@urv.cat francesc.serratosa@urv.cat
    Identificador de l'autor: 0000-0002-1241-1646 0000-0001-6112-5913
    Data d'alta del registre: 2024-10-12
    Versió de l'article dipositat: info:eu-repo/semantics/publishedVersion
    Enllaç font original: https://www.eurekaselect.com/182468/article
    Programa de finançament: : Marie Skłodowska-Curie Actions - European Union's Horizon 2020 research and innovation programme
    URL Document de llicència: https://repositori.urv.cat/ca/proteccio-de-dades/
    Referència a l'article segons font original: Current Topics In Medicinal Chemistry. 20 (18): 1582-1592
    Referència de l'ítem segons les normes 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
    Acrònim: MFP
    DOI de l'article: 10.2174/1568026620666200603122000
    Entitat: Universitat Rovira i Virgili
    Any de publicació de la revista: 2020
    Acció del programa de finançament: Martí i Franquès COFUND Doctoral Programme
    Tipus de publicació: Journal Publications
  • Paraules clau:

    Chemistry, Medicinal,Drug Discovery,Medicine (Miscellaneous)
    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
    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
  • Documents:

  • Cerca a google

    Search to google scholar