PMC:4331677 / 438-1545 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4331677","sourcedb":"PMC","sourceid":"4331677","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4331677","text":"Methods\nWe suppose that the ligand-target interactions are determined by ligand substructures as well as the physical-chemical properties of the binding sites. Therefore, we propose a fragment interaction model (FIM) to describe the interactions between ligands and targets, with the purpose of facilitating the chemical interpretation of ligand-target binding. First we extract target-ligand complexes from sc-PDB database, based on which, we get the target binding sites and the ligands. Then we represent each binding site as a fragment vector based on a target fragment dictionary that is composed of 199 clusters (denoted as fragements in this work) obtained by clustering 4200 trimers according to their physical-chemical properties. And then, we represent each ligand as a substructure vector based on a dictionary containing 747 substructures. Finally, we build the FIM by generating the interaction matrix M (representing the fragment interaction network), and the FIM can later be used for predicting unknown ligand-target interactions as well as providing the binding details of the interactions.","divisions":[{"label":"title","span":{"begin":0,"end":7}}],"tracks":[]}