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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.
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 ...
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 ...
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.
A cavity, or region where the molecular docking will take place, is set around the binding site, which is the region in the receptor protein where the ligand attaches to. After specifying the cavity, molecular docking settings are configured and the program is run in order to determine the binding energy of the complex.
Energy-based multiple structural alignment of proteins: Cα: Multi: No: server: C. Micheletti & H. Orland: 2009 MSVNS for MaxCMO A simple and fast heuristic for protein structure comparison: C-Map: Pair: No: site: D. Pelta et al. 2008 Structal Least Squares Root Mean Square deviation minimization by dynamic programming: Cα: Pair: No: server ...
AutoDock for docking of the ligand to a set of grids describing the target protein; AutoGrid for pre-calculating these grids. Usage of AutoDock has contributed to the discovery of several drugs, including HIV1 integrase inhibitors. [6] [7] [9] [10]
Protein–ligand docking: License: Proprietary software: Website: www.schrodinger.com /products /glide: Glide is a molecular modeling software for docking of small ...