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. 2019 Sep 15;20(18):4574. doi: 10.3390/ijms20184574

Table 1.

Molecular docking software.

Software Posing Scoring Availability Reference
Vina Iterated Local Search + BFGS Local Optimiser Empirical/Knowledge-Based Free (Apache License) Trott, 2010 [3]
AutoDock4 Lamarckian Genetic Algorithm, Genetic Algorithm or Simulated Annealing Semiempirical Free (GNU License) Morris, 2009; Huey, 2007 [31,32]
Molegro/MolDock Differential Evolution (Alternatively Simplex Evolution and Iterated Simplex) Semiempirical Commercial Thomsen, 2006 [9]
Smina Monte Carlo stochastic sampling + local optimisation Empirical (customisable) Free (GNU License) Koes, 2013 [33]
Plants Ant Colony Optimisation Empirical Academic License Korb, 2007; Korb, 2009 [34,35]
ICM Biased Probability Monte Carlo + Local Optimisation Physics-Based Commercial Abagyan, 1993; Abagyan, 1994 [36,37]
Glide Systematic search + Optimisation (XP mode also uses anchor-and-grow) Empirical Commercial Friesner, 2004 [38]
Surflex Fragmentation and alignment to idealised molecule (Protomol) + BFGS optimisation Empirical Commercial Jain, 2003; Jain 2007 [39,40]
GOLD Genetic Algorithm Physics-based (GoldScore), Empirical (ChemScore, ChemPLP) and Knowledge-based (ASP) Commercial Jones, 1997; Verdonk 2003 [6,7]
GEMDOCK Generic Evolutionary Algorithm Empirical (includes pharmacophore potential) Free (for non-commercial research) Yang, 2004 [41]
Dock6 Anchor-and-grow incremental construction Physics-based (several other options) Academic License Allen, 2015 [42]
GAsDock Entropy-based multi-population genetic algorithm Physics-based * Li, 2004 [43]
FlexX Fragment-Based Pattern-recognition (Pose Clustering) + Incremental Growth Empirical Commercial Rarey, 1996; Rarey, 1996b [8,44]
Fred Conformer generation + Systematic rigid body search Empirical (defaults to Chemgauss3) Commercial McGann, 2011 [45]
DockThor Steady-state genetic algorithm (with Dynamic Modified Restricted Tournament Selection method) Physics-based + Empirical Free (Webserver) De Magalhães, 2014 [4,25]

* Availability is unclear.