Modules

Align proteins, cavities or ligands. Computes the transformation that superposes one molecule onto another and applies it to as many other files as you like — the step that turns a GRIM match into a structure you can look at.

Converts the 3D structure of a protein (or nucleic acid) – ligand complex into a residue-based interaction fingerprint, and computes pairwise similarities between fingerprints. The standard way to rank docking poses on the interactions they reproduce.

Lists in a table the non-covalent interactions of a 3D structure — hydrophobic, aromatic, hydrogen bonds, ionic bonds, halogen bonds and more — and encodes each as a pseudoatom, giving a representation that no longer depends on the binding site.

Converts complexes into generic 3D graphs and computes pairwise similarities by finding their largest common subgraph. Detects that two unrelated proteins bind their ligands the same way, and returns the alignment that proves it.

Detects cavities at the surface of a protein and estimates their druggability, with or without a bound ligand to point at. Can also emit the cavity as a pharmacophore ready to screen with.

Various goodies: computes buried surface areas, and fragments a protein-bound ligand according to RECAP rules while keeping its protein context.