List of protein-ligand docking software

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
DOCK	1988	University of California-San Francisco	Based on Geometric Matching Algorithm
FlexAID	2015	University of Sherbrooke	Target side-chain flexibility and soft scoring function, based on surface complementarity
LeDock	2016	Lephar	Program for fast and accurate flexible docking of small molecules into a protein
Glide	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
Molecular Operating Environment	2008	Chemical Computing Group	Docking application within MOE; choice of placement methods and scoring functions
rDock	1998 2006 2012	Vernalis R&D University of York University of Barcelona	HTVS of small molecules against proteins and nucleic acids, binding mode prediction
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