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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.
Comprehensive life science modeling and simulation suite of applications focused on optimizing drug discovery process: small molecule simulations, QM-MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. Proprietary, trial available
The library delegates many calculations to more specialized third-party software. It currently utilizes 15 external applications, including X-PLOR, Hex, T-Coffee, DSSP and MODELLER. The latest Biskit version, 2.4.0, was released on 4 Mar 2012. It was originally developed at the Pasteur Institute.
The goal of protein–ligand docking is to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme. [1] Pharmaceutical research employs docking techniques for a variety of purposes, most notably in the virtual screening of large databases of available chemicals in order to select ...
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.
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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HxD is a freeware hex editor, disk editor, and memory editor developed by Maël Hörz for Windows. It can open files larger than 4 GiB and open and edit the raw contents of disk drives, as well as display and edit the memory used by running processes. Among other features, it can calculate various checksums, compare files, or shred files. [1]