Software:List of protein-ligand docking software
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Short description: none
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. This table is comprehensive but not complete.
| Program | Year Published | Organisation | Description | Webservice | License |
|---|---|---|---|---|---|
| AutoDock | 1990 | The Scripps Research Institute | Automated docking of ligand to macromolecule by Lamarckian Genetic Algorithm and Empirical Free Energy Scoring Function | No | Open source (GNU GPL) |
| DOCK | 1988 | University of California-San Francisco | Based on Geometric Matching Algorithm | No | Freeware for academic use |
| FlexAID | 2015 | University of Sherbrooke | Target side-chain flexibility and soft scoring function, based on surface complementarity | No | Open source (Apache License) |
| LeDock | 2016 | Lephar | Program for fast and accurate flexible docking of small molecules into a protein | No | Freeware for academic use |
| Glide[1] | 2004 | Schrödinger, Inc. | Glide is a ligand docking program for predicting protein-ligand binding modes and ranking ligands via high-throughput virtual screening. Glide utilizes two different scoring functions, SP and XP GlideScore, to rank-order compounds. Three modes of sampling ligand conformational and positional degrees of freedom are available to determine the optimal ligand orientation relative to a rigid protein receptor geometry | No | commercial |
| Molecular Operating Environment (MOE) | 2008 | Chemical Computing Group | Docking application within MOE; choice of placement methods (including alpha sphere methods) and scoring functions (including London dG) | No | Commercial |
| rDock | 1998 (commercial) 2006 (academic)[2] 2012 (open source)[3] |
Vernalis R&D (commercial) University of York (academic) University of Barcelona (open source) |
HTVS of small molecules against proteins and nucleic acids, binding mode prediction | No | Open source (GNU LGPL) (formerly commercial, academic) |
| SEED | 1999 | University of Zurich | Automated docking of fragments with evaluation of free energy of binding including electrostatic solvation effects in the continuum dielectric approximation (generalized Born) | No | Open source (GNU GPL) |
References
- ↑ "Gliding to success.". Nature Reviews Drug Discovery 3 (4): 299. April 2004. doi:10.1038/nrd1364.
- ↑ "rDock". http://www.ysbl.york.ac.uk/rDock/.
- ↑ "About | rDock" (in en-US). http://rdock.sourceforge.net/about/.
External links
- "Protein-ligand docking bioinformatics tools | Interaction analysis" (in en). https://omictools.com/protein-ligand-docking-category.
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