A toolkit for covalent docking with GOLD: from automated ligand preparation with KNIME to bound protein-ligand complexes.
Journal
Bioinformatics advances
ISSN: 2635-0041
Titre abrégé: Bioinform Adv
Pays: England
ID NLM: 9918282081306676
Informations de publication
Date de publication:
2022
2022
Historique:
received:
16
05
2022
revised:
22
10
2022
accepted:
28
11
2022
entrez:
26
1
2023
pubmed:
27
1
2023
medline:
27
1
2023
Statut:
epublish
Résumé
Current covalent docking tools have limitations that make them difficult to use for performing large-scale structure-based covalent virtual screening (VS). They require time-consuming tasks for the preparation of proteins and compounds (standardization, filtering according to the type of warheads), as well as for setting up covalent reactions. We have developed a toolkit to help accelerate drug discovery projects in the phases of hit identification by VS of ultra-large covalent libraries and hit expansion by exploration of the binding of known covalent compounds. With this application note, we offer the community a toolkit for performing automated covalent docking in a fast and efficient way. The toolkit comprises a KNIME workflow for ligand preparation and a Python program to perform the covalent docking of ligands with the GOLD docking engine running in a parallelized fashion. The KNIME workflow entitled ' Supplementary data are available at
Identifiants
pubmed: 36699353
doi: 10.1093/bioadv/vbac090
pii: vbac090
pmc: PMC9722222
doi:
Types de publication
Journal Article
Langues
eng
Pagination
vbac090Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
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