PMC:5056895 / 9553-10395 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5056895","sourcedb":"PMC","sourceid":"5056895","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5056895","text":"Ligand preparation and molecular docking\nChemical structures of ligands (amodiaquine, prochlorperazine, quinacrine, and berberine) used in this study were retrieved from the PubChem database [32]. PDBQT files of ligands and receptor molecules (NS3) was prepared. Then the protein-ligand docking studies were performed using the AutoDock Vina program [26]. It is one of the widely use method for protein-ligand docking. AutoDock Vina significantly improves the average accuracy of the binding mode predictions. For the input and output, Vina uses the PDBQT molecular structure file format. Here PDBQT file of four drugs were taken as ligand and PDBQT file of NS3 was taken as protein. These drug compounds were docked with NS3 protein of ZIKV and NS3 protein of DENV around its important binding site residues such as His51, Asp75, and Ser135.","divisions":[{"label":"Title","span":{"begin":0,"end":40}}],"tracks":[{"project":"2_test","denotations":[{"id":"27729840-19933261-44841864","span":{"begin":192,"end":194},"obj":"19933261"},{"id":"27729840-19499576-44841865","span":{"begin":351,"end":353},"obj":"19499576"}],"attributes":[{"subj":"27729840-19933261-44841864","pred":"source","obj":"2_test"},{"subj":"27729840-19499576-44841865","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec93bc","default":true}]}]}}