Yisheng Wang, Youjin Xiong, Eduardo Alejandro Lozano Garcia, Yiqing Wang, Christopher J.Molecular Pharmaceutics 2022, Article ASAP. Multi-Level High-Throughput Screening for Discovery of Ligands That Inhibit Insulin Aggregation. Rit Pratik Mishra, Surbhi Gupta, Anurag Singh Rathore, Gaurav Goel.This article is cited by 125 publications. The obtained results probably will be useful for future docking studies in deciding which program to use. However, the short option is the best solution for carrying out Vina docking. In addition, the best docking option for performing the AD4 approach is the long option. There are 16 complexes for which both the AD4 and Vina protocols fail to produce a reasonable correlation with respected experiments so both are not suitable to use to estimate binding free energies for these cases. However, interestingly, AD4 shows a better performance than Vina over 21 considered targets, whereas the Vina protocol is better than the AD4 package for 10 other targets. Our calculation results are in good agreement with a previous study that the Vina approach converges much faster than AD4 one. Docking calculations were performed for these complexes using both Autodock4 and Autodock Vina with different docking options related to computing resource consumption and accuracy. In this study, we selected 800 protein–ligand complexes for which both PDB structures and experimental binding affinity are available. It is of great interest to compare the success rate of the two docking software programs for a large and diverse set of protein–ligand complexes. Autodock4 and Autodock Vina are two commonly used open-source and free software tools to perform this task, and each has been cited more than 6000 times in the last ten years. In the initial stage of a drug discovery project, this information is often obtained by using molecular docking methods. The binding pose and affinity between a ligand and enzyme are very important pieces of information for computer-aided drug design.
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