Docking

Docking is an in silico technique of determining the molecular structure of complexes formed by two or more molecules without the need for experimental measurement. With the rapid increase in available structures biomolecules, this technique can be exploited to model complexes of biological interest. Docking is an invaluable tool for drug designing. Computational resources of this area have been classified in following categories:

Downloads

Server	Description
AutoDock	Predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
DOCK	Predict binding modes of small molecule-protein complexes.
DOT	Dock macromolecules including Proteins,DNA,RNA.
3D-DOCK	Predict protein-protein docking.
GRAMM	Protein-Protein docking and Protein-Ligand docking.
Hex	Protein docking using polar Fourier correlations.
ZDOCK	Rigid body docking program.

Webservers

Server	Description
RosettaDock	Predicts the structure of a protein-protein complex from the individual structures of the monomer components.
Cluspro	Filtering, Clustering, and Ranking Protein-Protein Complexes.
ZDOCK	Fast Fourier Transform based protein docking program.
HEX	Protein Docking Using Polar Fourier Correlations.

Webservers

Server	Description
Q-site finder	Ligand binding site prediction method.
BIND	Bimolecular interaction network database.
Binding Interface Database	Organizes the vast amount of protein interaction information into tables, graphical contact maps and descriptive functional profiles.
KEGG LIGAND Database	KEGG LIGAND database.
SCOPPI	Database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions.
CAPRI	Critical assessment of Prediction of Interactions

Libraries

Biopython