Table 1.
A list of widely used tools for docking.
| No. | Software/Tools | Algorithm | Scoring Term | Advantages | Ref. |
|---|---|---|---|---|---|
| 1. | Molecular Operating Environment (MOE) | High-Speed α shapes algorithms | London dG, FlexX, DrugScore, Mcdock | Customizable, available source-code, gives binding affinity score, shows interacting amino acids with position, and is user-friendly. | [25] |
| 2. | PyRx | Lamarckian genetic algorithm | Binding energy, Internal energy, Internal energy, Unbound energy | Temperature Resistance. Pyrex’s excellent thermal properties at both high and low temperatures are one of its key features. | [26] |
| 3. | Glide (Grid-based Ligand Docking with Energetics) |
Monte Carlo | Glide score | Lead discovery and lead optimization | [27] |
| 4. | AutoDock | Lamarckian genetic algorithm | Empirical free-energy function | Adaptability to user-defined input | [28] |
| 5. | GOLD (Genetic Optimization for Ligand Docking) | Genetic algorithm | GoldScore, ChemScore, ASP (Astex Statistical Potential), CHEMPLP (Piecewise Linear Potential), User-defined | Allows atomic overlapping between protein and ligand | [29] |
| 6. | Surflex | Surflex-Dock search Algorithm |
Bohm’s scoring function | High accuracy level by extending force fields | [30] |
| 7. | FlexX | Incremental reconstruction | Modified Bohm scoring function | Provides a large number of conformations | [31] |
| 8. | ICM (Internal Coordinate Modeling) |
Monte Carlo minimization | Virtual library screening scoring function | Allows side chain flexibility to find a parallel arrangement of two rigid helixes | [32] |
| 9. | MVD (Molegro Virtual Docker) | Evolutionary algorithm | MolDock score | High accuracy level of predicting binding mode | [33] |
| 10. | Fred (Fast Rigid Exhaustive Docking) |
Exhaustive search algorithm | Gaussian scoring function | Nonstochastic approach to examine all possible poses within a protein active site | [34] |
| 11. | LigandFit | Monte Carlo method | LigScore, Piecewise Linear Potential (PLP), Potential of Mean Force (PMF) | Generates good hit rates based on LigScore | [35] |
| 12. | FITTED (Flexibility Induced Through Targeted Evolutionary Description) | Genetic algorithm | Potential of Mean Force (PMF), Drug Score | Analyzes the effect of water molecules on protein–ligand complexes | [36] |
| 13. | GlamDock | Monte Carlo method | ChillScore | Provides provision of two-dimensional analysis to screen ligands by targeting protein | [37] |
| 14. | iGEMDOCK | Genetic algorithm | Empirical scoring function | Integrates the structure-based virtual screening and post-screening analysis. Provides a graphical integrated environment for virtual screening | [38] |