The KRIPO (Key Representation of Interaction in POckets) method for quantifying the similarities of binding site subpockets is based on fuzzy 3-point pharmacophore fingerprints38. This approach provides a useful method for comparing both whole binding sites and binding site subregions, and is valuable in predicting bioisosteres based only on the 3D properties of the protein. Comparisons can be made across protein families, leading to a higher number of diverse results.
KripoDB is the library to interact with Kripo fragment, fingerprint and similarity data files.
- Pocket, binding site of the ligand in the protein of a crystal structure
- Fragment, part of the ligand
- Subpocket, part of the protein pocket which binds with the fragment
- Pharmacophore, amino acids of subpocket translated to abstract points of a pharmacophore type like hydrogen bond donor, hydrophobe, negative charge, etc.
- Fingerprint, fingerprint of structure-based pharmacophore of subpocket
- Similarity matrix, similarities between all fingerprint pairs calculated using the modified tanimoto similarity index
- Kripo fragment identifier, used as identifier for fragment, subpocket and fingerprint
All fragments form all proteins-ligand complexes in PDB compared with all. A Kripo data set consists of the following:
- fragments.sqlite - Fragments sqlite database
- Similarity webservice - Webservice to query for similar fragments.
- fingerprints.*.fp.gz - Fragment fingerprints are available on request.
See Data update chapter of documentation for data set build instructions.