Autodock Vina was employed to carry out individual molecular docking as well as multiple ligand simultaneous docking. The results were analyzed in terms of binding energy and different interacting residues. Interestingly, (3) displayed a higher binding affinity towards all the aging and antioxidant ...
Optional static variables to be used as inputs #the path and file name of the ligand (for debug purposes only) ligand #The folder where ligands are stored.About This project will automate the processing of multiple ligands in autodock vina using a python script Resources Readme Activity ...
VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high-throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with ...
Utilising network pharmacology and molecular dockingtoexplore the mechanism of Sangbaipi Decoction in the treatment of acute exacerbation of chronic obstru... protein receptors through AutoDock Vina soft-ware,and the 2D ligand-protein interaction diagramsare drawn through LigPlot 2.2 software.ResultsThere...
The Autodock Vina program35 was used for docking iP-NBD ligand into the set of AHK structures obtained from homology modelling. A 15 Å box centred at the original ligand binding position was used. The exhaustiveness parameter was set to 20. Competitive binding assay in E. coli strains ...
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J. Comput. Chem., 31 (2) (2010), pp. 455-461 CrossrefGoogle Scholar [24] R.A. Laskowski, M.B. Swindells LigPlot+: multiple ligand-protein interaction diagra...
Trott O, Olson A (2010) AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461 Article CAS PubMed PubMed Central Google Scholar Tsuchiya H, Doki S, Takemoto M, Ikuta T, Higuchi T, Fuk...
State-of-the-art protein-ligand docking methods are generally limited by the traditionally low accuracy of their scoring functions, which are used to predict binding affinity and thus vital for discriminating between active and inactive compounds. Despite intensive research over the years, classical sco...
observed to be similar to the co-crystal structure of GAD67, which involves the binding of an original ligand PLP-γ-aminobutyric acid (PLP-GABA) (Supplementary Fig.6); the similar binding modes indicate that residues in the active site of GAD67, which interact with PLP-GABA, can also be...
Multiple-seedings of AutoDock Vina and in situ minimization were to account for the non-deterministic nature of AutoDock Vina search algorithm and binding site flexibility, respectively. ADME/T and interaction analyses were also done on the top hits via FAFDRUG3 web server and Discovery Studio ...