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- W4310361545 abstract "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 ‘Evotec_Covalent_Processing_forGOLD.knwf’ for the preparation of the ligands is available in the KNIME Hub https://hub.knime.com/emilie_pihan/spaces. Supplementary information Supplementary data are available at Bioinformatics Advances online." @default.
- W4310361545 created "2022-12-09" @default.
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- W4310361545 date "2022-01-01" @default.
- W4310361545 modified "2023-10-03" @default.
- W4310361545 title "A toolkit for covalent docking with GOLD: from automated ligand preparation with KNIME to bound protein–ligand complexes" @default.
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- W4310361545 doi "https://doi.org/10.1093/bioadv/vbac090" @default.
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