Here we collect some information before we start the Covalentizer process.
After receiving this information, the Covalentizer algorithm will be applied to it.
It includes the following steps:
Check if there are any cysteines in proximity to the ligand.
Break down the ligand into fragments.
Covalentize the fragments.
Dock the covalentized fragments to the nearby cysteines, including multiple rotamers of the cysteines.
Calculate RMSD of the maximal common substructure between the original ligand and the covalentized fragment.
Produce a result folder for any docked fragment with RMSD of < 1.5 Å.
Send you the results via the provided email address.
For more information regarding the algorithm, please read https://www.biorxiv.org/content/10.1101/2020.09.21.299776v1