Fragment-Based Ligand-Protein Contact Statistics: Application to Docking Simulations.
fragment-based contact statistics
molecular docking
scoring functions
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
21 May 2019
21 May 2019
Historique:
received:
02
05
2019
revised:
16
05
2019
accepted:
17
05
2019
entrez:
24
5
2019
pubmed:
24
5
2019
medline:
4
12
2019
Statut:
epublish
Résumé
In this work, the information contained in the contacts between fragments of small-molecule ligands and protein residues has been collected and its exploitability has been verified by using the scoring of docking simulations as a test case for bringing about a proof of concept. Contact statistics between small-molecule fragments and binding site residues were collected and analyzed using a dataset composed of 200,000+ binding sites and associated ligands, derived from the database of the LIBRA ligand binding site recognition software, as a starting point. The fragments were generated by applying the decomposition algorithm implemented in BRICS. A simple "potential" based on the contact frequencies was tested against the CASF-2013 benchmark; its performance was then evaluated through the rescoring of docking poses generated for the DUD-E dataset. The results obtained indicate that this approach, its simplicity notwithstanding, yields promising results that are comparable, and in some cases, superior, to those obtained with other, more complex scoring functions.
Identifiants
pubmed: 31117183
pii: ijms20102499
doi: 10.3390/ijms20102499
pmc: PMC6567162
pii:
doi:
Substances chimiques
Ligands
0
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Ministero dell'Istruzione, dell'Università e della Ricerca
ID : Dipartimenti di Eccellenza; Legge 232/2016, Articolo 1, Comma 314-337
Organisme : Ministero dell'Istruzione, dell'Università e della Ricerca
ID : PRIN no. 2017483NH8
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