MEDP-Fragmentor

MEDP-Fragmentor is part of the MED-SuMo fragment-based technology and performes the generation of the MED-SuMo fragment database from a database like the PDB

 

The MED-portions are encoded in the MED-SuMo fragment database which is ready to be searched and browsed with MED-SuMo. These 3D patterns, called MED-Portions, include chemical moieties which are matching molecules from a chemical library and substructures of protein-bound ligand. MED-Portions, which are the MED-SuMo representation of protein-fragment patterns defined by several criteria: (1) a chemical moiety where atoms are topologically matching with a molecule from molecular libraries, e.g. synthetically accessible molecules or building blocks, (2) open valences filled by ‘dummy atoms’ that indicate where it was connected in the original ligand, and (3) the protein interaction surface surrounding that chemical moiety described by the MED-SuMo Surface Chemical Features (SCFs).


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