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:

1 Check if there are any cysteines in proximity to the ligand.
2 Break down the ligand into fragments.
3 Covalentize the fragments.
4 Dock the covalentized fragments to the nearby cysteines, including multiple rotamers of the cysteines.
5 Calculate RMSD of the maximal common substructure between the original ligand and the covalentized fragment.
6 Produce a result folder for any docked fragment with RMSD of < 1.5 Å.
7 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.