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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.
One approach uses a matching technique that describes the protein and the ligand as complementary surfaces. [6] [7] [8] The second approach simulates the actual docking process in which the ligand-protein pairwise interaction energies are calculated. [9] Both approaches have significant advantages as well as some limitations. These are outlined ...
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 ...
LeDock is a molecular docking software, designed for protein-ligand interactions, that is compatible with Linux, macOS, and Windows. [2] [3] [4] The software can run as a standalone programme or from Jupyter Notebook. [5] It supports the Tripos Mol2 file format.
Rosetta@home aims to predict protein–protein docking and design new proteins with the help of about fifty-five thousand active volunteered computers processing at over 487,946 GigaFLOPS on average as of September 19, 2020. [4] Foldit, a Rosetta@home videogame, aims to reach these goals with a crowdsourcing approach.
PyRx provides a nice GUI for running virtual screening with AutoDock. PyRx includes a docking wizard and you can use it to run AutoDock Vina in the Cloud or HPC cluster. [25] POAP is a shell-script-based tool which automates AutoDock for virtual screening from ligand preparation to post docking analysis. [26]
CRIP: Computational resources for predicting protein–macromolecular interactions (CRIP) was developed to provide resources related to interaction. This site maintains a large number of resources on the interaction of proteins that includes protein–protein, protein–DNA, protein–ligand, protein–RNA.
rDock (previously RiboDock) is an open-source molecular docking software that be used for docking small molecules against proteins and nucleic acids. It is primarily designed for high-throughput virtual screening and prediction of binding mode.