Computational Drug Discovery and Design

Table 1
A summary of global docking programs

Software Search algorithm Scoring function

Reference

(s)

ATTRACT Randomized search LJ-type effective potentials and

electrostatics

[18]

PatchDock/

SymmDock

Local shape match Geometric shape complementarity [19]

FTDOCK FFT-based correlation Shape complementarity and

electrostatic interactions

[20]

GRAMM FFT-based correlation Shape and hydrophobic match [21]

GRAMMX FFT-based correlation Soft Lennard–Jones potential,

evolutionary conservation of

predicted interface, statistical

residue–residue preference,

volume of the minimum, empirical

binding free energy and atomic

contact energy

[22]

MolFit FFT-based correlation Geometric complementarity,

hydrophobic complementarity,

and electrostatic interactions

[23–25]

DOT FFT-based correlation van der Waals and electrostatic

energies

[26, 27]

ZDOCK FFT-based correlation Shape complementarity,

electrostatics, and knowledge-

based pair potentials

[28]

PIPER FFT-based correlation Shape complementarity, electrostatic

interactions, and knowledge-based

pair potentials

[29]

SDOCK FFT-based correlation van der Waals attractive potential,

geometric collision, electrostatic

potential, and desolvation energy

[30]

ClusPro FFT-based correlation Shape complementarity, electrostatics

and desolvation energy

[31, 32]

HEX SFT-based correlation Surface complementarity and

electrostatics

[33]

FRODOCK SFT-based correlation van der Waals, electrostatics, and

desolvation

[34]

HADDOCK Randomization of orientations and

rigid body energy minimization

followed by semi-rigid simulated

annealing in torsion angle space,

and finally refinement in

Cartesian space with explicit

solvent

Sum of intermolecular van der Waals,

electrostatic, ambiguous

interaction restraint energy, the

buried surface area and the

desolvation energy

[35, 36]

Protein-Protein Docking 289