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AutoDock Vina is a successor of AutoDock, significantly improved in terms of accuracy and performance. [3] It is available under the Apache license . Both AutoDock and Vina are currently maintained by Scripps Research , specifically the Center for Computational Structural Biology (CCSB) led by Dr. Arthur J. Olson [ 4 ] [ 5 ]
The number of notable protein-ligand docking programs currently available is high and has been steadily increasing over the last decades. The following list presents an overview of the most common notable programs, listed alphabetically, with indication of the corresponding year of publication, involved organisation or institution, short description, availability of a webservice and the license.
Several protein–ligand docking software applications that calculate the site, geometry and energy of small molecules or peptides interacting with proteins are available, such as AutoDock and AutoDock Vina, rDock, FlexAID, Molecular Operating Environment, and Glide. Peptides are a highly flexible type of ligand that has proven to be a ...
LeDock utilizes a simulated annealing and genetic algorithm approach for facilitating the docking process of ligands with protein targets. The software employs a knowledge-based scoring scheme that is derived from extensive prospective virtual screening campaigns.
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]
FlexAID has been shown to outperform existing widely used software such as AutoDock Vina and FlexX in the prediction of binding poses. This is particularly true in cases where target flexibility is crucial, such as is likely to be the case when using homology models.
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First screened using AutoDock Vina, the top-scoring 500 were then analysed using BEDAM. After further screening, 24 of these were selected to perform thermal shift assays . 2 compounds appear to bind at the HIV-1 Capsid dimmer interface, possibly by occupying a new sub-pocket that has not been exploited by any existing HIV-1 capsid inhibitors.