A toolkit for covalent docking with GOLD: from automated ligand preparation with KNIME to bound protein-ligand
Laurianne David1, Anissa Mdahoma1, Natesh Singh1
1Evotec SE, Molecular Architects, Integrated Drug Discovery, Toulouse 31036, France.
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.
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