Macromolecules surface similarities detection at PDB scale is a technology breakthrough to discover a wealth of drug design data. Exploit all known macromolecule structures with MED-SuMo
Searching, browsing and superimposing 3D macromolecules structures
Site mining and drug repurposing
Because local similarities between proteins are more likely to occur than a whole binding site similarity, we've developped a computational fragment-based approach at PDB scale by protein local similarity. It is based on MED-SuMo/MED-Ligand and MED-Portions where a MED-Portion is a new 3D pattern encoding protein-fragment binding sites. These 3D patterns include chemical moieties which are matching molecules from a chemical library and substructures of protein-bound ligand from the PDB. Populate binding sites with MED-Portion chemical moities by target hopping with the computational fragment based drug design protocol.
Hybridise the MED-Portion chemical moieties into 3D molecules with MED-Ligand, a de novo like protocol, and use the hybrids to query the molecule database from suppliers and find real molecules to test.