ChemServerBinding pocket detection and pose analysis
Before docking, find where a ligand can bind and how big it may be. After docking, check whether the pose makes sense and which residues hold it in place.
1. Pocket scan and sizing
Detect cavities on the protein surface with fpocket or the built in scanner, see each pocket's volume, and get the range of ligand volumes that fit it. Generate pocket constrained ligand variants that fill a chosen fraction of the pocket.
2. Consensus site map
Combine pocket detection with an optional co crystal ligand and the residues you know are important, to agree on one binding site.
3. Pockets across several structures
Bring several PDB structures of the same protein into a common frame and match their pockets, useful for ensemble docking and for spotting pockets that open in only some structures.
4. Pose quality and pharmacophore
Check a docked pose for clashes and sensible contacts, list its pharmacophore features with RDKit and build an interaction fingerprint of the residues it touches.
5. Mutation impact
Alanine scanning and charge flip scans (Asp, Glu, Lys, Arg, His) estimate which pocket residues matter most for holding the ligand. A higher impact score means more contacts are lost when that residue is mutated.
Straight into docking
Any pocket you pick here can be applied as the grid box in Batch Docking.