Table 1.
Some commonly used docking software
| Software | Algorithm features | Home page |
|---|---|---|
| AutoDock (Morris et al. 1998; Morris et al. 2009) | Lamarckian Genetic Algorithm and empirical binding free energy function | http://autodock.scripps.edu/ |
| AutoDock Vina (Olson 2010) | Iterated local search global optimizer, with sophisticated gradient optimization method in its local optimization procedure. The derivation of its scoring function combines certain advantages of knowledge-based potentials and empirical scoring functions | http://vina.scripps.edu/ |
| rDock (Sergio et al. 2014) | Evolved from RiboDock, rDock uses a combination of stochastic and deterministic search techniques to generate low-energy ligand pose. rDock includes fast intermolecular scoring functions (vdW, polar, desolvation) and implements several pseudo-energy scoring functions that are added to the total scoring function under optimization and a restricted search protocol | http://rdock.sourceforge.net |
| Dock 6 (William et al. 2015) | Anchor-and-grow search algorithm is a breadth-first method for small-molecule conformational sampling. It utilizes a footprint similarity scoring function | http://dock.compbio.ucsf.edu/ |
| LeDock (Zhao et al. 2013; Zhao et al. 2011) | Simulated annealing and genetic algorithm optimization. The scoring function, based on AutoDock 4 scoring function, calculates hydrogen bonding penalty associated with ligand binding to improve binding | http://lephar.com/ |
| Glide (Friesner et al. 2004) | Complete systematic search of the conformational, orientational, and positional space of the docked ligand. Its scoring function, named as Emodel, combines empirically based ChemScore function, force-field-based terms from the Coulomb and vdW interaction energies between the ligand and the receptor, and the solvation model | http://www.schrodinger.com/ |
| Gold (Jones et al. 1997) | Genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein. Its scoring function comprised terms for hydrogen bonding, pairwise dispersion potentials, and molecular mechanics terms | http://www.ccdc.cam.ac.uk/ |
| FlexX (Rarey et al. 1996) | Fragment growth method to find the best conformation and empirical scoring function to compute the binding affinity | https://www.biosolveit.de/products/ |
| Surflex (Jain et al. 2003) | Employs a “protomol” that can be automatically generated or user defined to generate putative poses of molecules or molecular fragments. The scoring function, based on Hammerhead scoring function, uses an updated and re-parameterized empirical scoring function | http://www.tripos.com/ |
| LigandFit (Krammer et al. 2005; Venkatachalam et al. 2003) | Shape-directed docking methodology. Ligand conformations are generated by a Monte Carlo conformational search for generating ligand poses consistent with the active site shape. Its scoring function is called LigScore, which consist of three distinct terms that describe the van der Waals interaction, the polar attraction, and the desolvation penalty | https://www.3dsbiovia.com/ |