Predicting the structure of protein–protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes. Following are the tools to predict the structure of protein–protein complexes:
Global rigid search: FFTShape complementarity and electrostatics
Re-scoring and clustering. Refinement of interface side-chains
Global rigid search in ensamble
Shape complementarity and Lennard–Jones potential
Side chain and backbone dihedral refinement
Global rigid search: FFTShape complementarity, electrostatics and VDWNone
Global rigid searchShape complementarity, hydrogen bonds and electrostatic
Integrated in VEGA
Global rigid search: FFT. smooth protein surface representation for soft docking
Shape complementarity and Lennard-Jones potential
Clustering of conformations
Global rigid search: FFT. smooth protein surface representation for soft docking
Shape complementarity and Lennard-Jones potentialminimization and re-scoring with multiple filters
Global rigid search: Fourier correlation of spherical harmonics
Shape complementarity
Global rigid searchElectrostatic ,VDW and desolvation energy termsMD simulated annealing refinement . Filtering based on external data.
Global rigid search: Monte CarloEmpirical scoring function
Clustering and selection of conformations. Refinement of interface side-chains and re-scoring
Global rigid search: FFTShape complementarity
Clustering of good solutions, filtering using a priori information and small, local rigid rotations around selected conformations
Global rigid searchShape complementarity and atomic desolvation energy
Clustering of conformations
Global rigid search:FFTShape complementarity
rescoring by binding electrostatics and desolvation energy
Local rigid search: Monte Carlo with low and high resolution structure representation levels
Different scoring parameters for the different resolutions
Global rigid search: FFTShape complementarity, desolvation energy, and electrostatics.
Energy minimization and re-scoringFree for academics
Point to note:
The proper treatment of flexibility in protein–protein docking is still an active field of research. You first should analyzed your proteins in order to define their conformational space and then choose the most suitable method for your docking problem.
