Algorithm for Extraction of Sub-Structure from Co-Crystallized PDB Ligand for Selective Targeting

ABSTRACT An algorithm has been introduced for extraction of sub-structure from co-crystallized ligand of complex PDB file. Algorithm utilized location of atoms in 3D domain of complex of ligand & protein. It processed relative positioning of atoms for demarcation of influential part of ligand, which can provide potency to that ligand for binding with specific binding pocket of protein. Algorithm was validated with ligands co-crystallized with enzymes of different classes. Extracted sub-structures were validated (via evidence from database & literature) for selectivity towards one or more targets of same family.