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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]
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.
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
Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications. Molekel: MM XRD: Free open-source: Java 3D applet or standalone program: Ovito: MM XRD EM MD: Free open-source: Python [13 ...
Jeffrey Skolnick is an American computational biologist.He is currently a Georgia Institute of Technology School of Biology Professor, the Director of the Center for the Study of Systems Biology, the Mary and Maisie Gibson Chair, the Georgia Research Alliance Eminent Scholar in Computational Systems Biology, the Director of the Integrative BioSystems Institute, and was previously the ...
A protein–ligand complex is a complex of a protein bound with a ligand [2] that is formed following molecular recognition between proteins that interact with each other or with other molecules. Formation of a protein-ligand complex is based on molecular recognition between biological macromolecules and ligands, where ligand means any molecule ...