Table 1.
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.