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
AutoDockPredict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
DOCKPredict binding modes of small molecule-protein complexes.
DOTDock macromolecules including Proteins,DNA,RNA.
3D-DOCKPredict protein-protein docking.
GRAMMProtein-Protein docking and Protein-Ligand docking.
HexProtein docking using polar Fourier correlations.
ZDOCKRigid body docking program.


Webservers

Server Description
RosettaDockPredicts the structure of a protein-protein complex from the individual structures of the monomer components.
ClusproFiltering, Clustering, and Ranking Protein-Protein Complexes.
ZDOCKFast Fourier Transform based protein docking program.
HEXProtein Docking Using Polar Fourier Correlations.


Webservers

Server Description
Q-site finderLigand binding site prediction method.
BINDBimolecular interaction network database.
Binding Interface DatabaseOrganizes the vast amount of protein interaction information into tables, graphical contact maps and descriptive functional profiles.
KEGG LIGAND DatabaseKEGG LIGAND database.
SCOPPIDatabase of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions.
CAPRICritical assessment of Prediction of Interactions


Libraries

Biopython