molclaw-hdock-tool

Protein docking for virtual screening uses HDOCKlite to generate ranked protein-protein or protein-ligand complex models. You provide receptor and ligand PDB files, configure parameters like model count and rotation angle, and receive a run directory with ranked PDB outputs.

HDOCK is a docking algorithm used for structure-based screening to predict protein complex structures. It samples rotations and generates multiple ranked poses, outputting a unique run directory with top-N PDB models and summary metrics for downstream hit selection.

HDOCK supports both protein-protein and protein-ligand docking workflows. You upload receptor and ligand PDB files, optionally include site annotations, and the tool generates ranked complex models suitable for structure-based screening scenarios.

Preprocessing PDB files is required before running protein docking to ensure accurate results. You must upload properly prepared receptor and ligand PDB files to the server before execution, as the tool enforces mandatory local verification of all structure outputs.

Docking parameters are configurable by setting the nmax value for model count and adjusting the rotation sampling angle. You can also toggle complex generation and provide optional receptor or ligand site files to guide the docking process.

Docking outputs require mandatory download and local verification to ensure reproducibility. The tool generates a unique run directory containing ranked PDB models, Hdock.out, and summary metrics that must be validated locally before downstream structural analysis.