Table 1.
List of common docking programs.
| Program | Ligand Flexibility | Receptor Flexibility | Scoring Functions | Examples of Application |
|---|---|---|---|---|
| Glide (HTVS, SP and XP) [94,95,189] | Exhaustive ligand conformation search | Soft docking | Empirical | Discovery of novel fibroblast growth factor receptor 1 kinase inhibitors [190] and CDK5 inhibitors [191] |
| GOLD [93] | Genetic algorithm | Soft docking Ensemble docking Side-chain flexibility |
Goldscore (empirical) Chemscore (empirical) ChemPLP (empirical) ASP (knowledge based) |
Design of non-peptide MDM2 inhibitors [192] |
| Autodock 4 [193] | Genetic Algorithm Simulated Annealing Local Search Lamarckian Genetic Algorithm |
Side-chain flexibility | Semi-empirical free energy force field | Discovery of reversible NEDD8 activating enzyme inhibitor [194] |
| DOCK 6 [195] | Incremental construction algorithm | Rigid | Force field | Design and development of potent and selective dual BRD4/PLK1 Inhibitors [196] |
| Internal Coordinates Mechanics (ICM) [197] | Stochastic search (MC) | Side-chain flexibility (rotamer libraries) | Force field | Discovery of novel retinoic acid receptor agonist [198] and enoyl-acyl carrier protein reductase inhibitors in Plasmodium falciparum [199] |
| Surflex [200,201] | Incremental construction algorithm | Ensemble docking | Empirical | Discovery of novel inhibitors of Leishmania donovani γ-glutamylcysteine synthetase [202] |
| MOE [99,203,204,205] | Systematic (exhaustive) Stochastic High throughput Conformational Import (incremental construction + stochastic) [99] |
Rigid | ASE (empirical) Affinity dG (empirical) Alpha HB (empirical) GBVI/WSA (force field) |
Identification of novel monoamine oxidase B inhibitors [206] and Chk1 inhibitors [207] |
| FlexX [208,209] | Incremental construction algorithm | Rigid | Empirical | Identification of PKB inhibitors [210] and phosphodiesterase 4 inhibitors [211] |
| FRED [212,213] | Systematic (exhaustive) search, precomputed using Omega (using torsion and ring libraries) [138] | Rigid | Chemgauss 3 (empirical) Chemgauss 4 (empirical) |
Discovery of selective butyrylcholinesterase inhibitors [214] |
Abbreviations: ASP: Astex Statistical Potential; BRD4: Bromodomain 4; CDK5: Cyclin dependent kinase 5; ChemPLP: Piecewise Linear Potential; HTVS: high throughput virtual screening; MDM2: Mouse double minute 2 homolog; PKB: Protein kinase B; PLK1: Polo-like Kinase 1.