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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.
Suite of automated docking tools Linux, Mac OS X, SGI IRIX, and Windows: GPL: ... Free Biology Software – Free Software Directory – Free Software Foundation
POAP is a shell-script-based tool which automates AutoDock for virtual screening from ligand preparation to post docking analysis. [26] VirtualFlow allows to carry out ultra-large virtual screenings on computer clusters and the cloud using AutoDock Vina-based docking programs, allowing to routinely screen billions of compounds. [27]
Proprietary, free academic use, source code Beckman Institute: NWChem: No No Yes Yes No No Yes No No High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods Free open source, Educational Community License version 2.0 NWChem: Protein Local Optimization Program: No Yes Yes Yes ...
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] High-quality images and movies can be created.
FlexAID is a molecular docking software that can use small molecules and peptides as ligands and proteins and nucleic acids as docking targets. As the name suggests, FlexAID supports full ligand flexibility as well side-chain flexibility of the target.
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The program does not always perfectly predict the actual physical pose when evaluating the RMSD between candidates. In order to then evaluate the strength of a computer algorithm to predict protein docking, the ranking of RMSD among computer-generated candidates must be examined to determine whether the experimental pose actually was generated ...