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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.
List of gene prediction software; List of disorder prediction software; List of Protein subcellular localization prediction tools; List of phylogenetics software; List of phylogenetic tree visualization software; Category:Metagenomics_software; Structural biology software. List of molecular graphics systems; List of protein-ligand docking software
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
A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues Automated webserver and some downloadable programs RaptorX: remote homology detection, protein 3D modeling, binding site prediction
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 ...
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.
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]
The protein-ligand challenges were separated from SAMPL in SAMPL5 (2015-2016) [6] [7] and were distributed as the new Grand Challenges of the Drug Design Data Resource (D3R). [23] SAMPL5 allowed participants to make predictions of the binding affinities of three sets of host–guest systems: an acyclic CB7 derivative and two host from the octa ...