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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.
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]
Timetabling problems, such as designing a non-conflicting class timetable for a large university; ... Protein folding and protein/ligand docking [51] [52]
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 ...
The Molecular Operating Environment was developed by the Chemical Computing Group under the supervision of President/CEO Paul Labute. [3] Founded in 1994 [4] and based in Montreal, Quebec, Canada, this private company is dedicated to developing computation software that will challenge, revolutionize, and aid in the scientific methodology.
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
In bioinformatics, LIGPLOT is a computer program that generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input. [1] The LIGPLOT is used to generate images for the PDBsum resource that summarises molecular structure.
University of Delaware: models protein-ligand docking using the CHARMM program. Yes DrugDiscovery@home Independent [188] Drug design: Supported in silico drug design of chemical compounds for medicines in the fields of cancer and neurodegenerative diseases. [188] Yes Enigma@Home 2007-09-09 [189] Cryptography: Cryptography