ArticleBioinformatics advances2022
A toolkit for covalent docking with GOLD: from automated ligand preparation with KNIME to bound protein-ligand complexes.
Article in Bioinformatics advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- The covalent docking software landscape: features and applications in drug design.Briefings in bioinformatics · 2025Review
- Profiling Serine Hydrolases in the Leishmania Host-Pathogen Interactome Using Cell-Permeable Activity-Based Fluorophosphonate Probes.Chembiochem : a European journal of chemical biology · 2025Article
- Covalent-Allosteric Inhibitors: Do We Get the Best of Both Worlds?Journal of medicinal chemistry · 2025Review
- Molecular Dynamics and Other HPC Simulations for Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Article
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Authors and funding
7 authors.
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Abstract
Motivation: 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. Results: 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. Availability and implementation: The KNIME workflow entitled ' Supplementary information: Supplementary data are available at
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