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It was compared to AutoDock 4 on selecting active compounds against HIV protease, and was recommended for docking large molecules. As the successor of AutoDock 4, AutoDock Vina significantly improves the average accuracy of the binding mode predictions while running two orders of magnitude faster with multithreading. Following its initial release, several parallel implementations were developed using either multithreading or computer cluster –. AutoDock has contributed to the discovery of several drugs, including the first clinically approved HIV integrase inhibitor. How to check inhibition constant in autodock vina software#The AutoDock series – is the most cited docking software in the research community, with over 5,000 citations according to Google Scholar. To date, there are hundreds of docking programs. The latter is subsequently important to improve the potency and selectivity of binding. Docking can therefore be used not only to determine whether a ligand binds, but also to understand how it binds. Protein-ligand docking predicts the preferred conformation and binding affinity of a small ligand as non-covalently bound to the specific binding site of a protein. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. How to check inhibition constant in autodock vina free#Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. Without tedious software installation, users can submit jobs using our website. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. ![]()
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