Models covalent binding of a ligand to a given residue by the flexible side chain method. Multiple simulations are performed in parallel and evaluated by a physics-based scoring function; expected to take several minutes. Results include the best poses in PDB format and a CSV of their predicted binding affinities and related measurements.

Modeling is stochastic, so it may take more than one attempt even at high exhaustiveness to find the correct pose. Due to the nature of the modeling, suboptimal poses can be returned alongside optimal ones. Clearly unviable poses (e.g., floating out in solution) should be ignored.

Example use case: You want to evaluate a likely or known non-covalent ligand’s potential to be augmented with some covalent warhead(s).

Technology: Sieve Stack's proprietary molecular docking tool (undisclosed).

Limitations: The reaction presumed to induce covalent binding must be explicitly provided in SMARTS format; the SMARTS for several common covalent reactions are provided here.