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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.
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
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]
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 ...
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 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 ...
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 ...
Protein structure prediction, cellular signaling, protein aggregation, and drug design [259] Yes Predictor@home: 2004-05-04 [260] The Scripps Research Institute: Molecular biology Test and evaluate new algorithms and methods of protein structure prediction in the context of the Sixth Biannual CASP [261] experiment [262] Yes Primaboinca 2010-07 ...