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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.
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.
Fixed length and fixed angle drawing; Automatic alignment of figures; Detection of structures, text, and arrows, and their automatic placement; Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in a built-in library
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]
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. [7]
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.
The development of rDock started in 1998 in RiboTargets (later Vernalis (R&D) Ltd). [1] The software was originally called RiboDock. [2] The development went on until 2006 when the software was licensed to University of York for academic distribution and also maintenance.