2005, Vol. 33, Web Server issue | Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov1,2 and Haim J. Wolfson*
The article introduces two freely available web servers for molecular docking: PatchDock and SymmDock. PatchDock is a geometry-based algorithm designed to predict protein-protein and protein-small molecule interactions, focusing on shape complementarity. It efficiently searches for transformations that yield good molecular shape complementarity, ensuring wide interface areas and minimal steric clashes. The server allows users to input protein structures in PDB format or retrieve them from the Protein Data Bank, and provides a user-friendly interface for submitting requests and viewing results. SymmDock, on the other hand, is a specialized algorithm for predicting cyclically symmetric homomultimers. It restricts its search to symmetric transformations, making it particularly efficient for predicting complexes with $C_{n}$ symmetry. The server requires users to input the asymmetric unit (monomer) and the symmetry order, and it generates predictions for the entire multimer. Both servers are available at http://bioinfo3d.cs.tau.ac.il, offering efficient and user-friendly solutions for molecular docking problems.The article introduces two freely available web servers for molecular docking: PatchDock and SymmDock. PatchDock is a geometry-based algorithm designed to predict protein-protein and protein-small molecule interactions, focusing on shape complementarity. It efficiently searches for transformations that yield good molecular shape complementarity, ensuring wide interface areas and minimal steric clashes. The server allows users to input protein structures in PDB format or retrieve them from the Protein Data Bank, and provides a user-friendly interface for submitting requests and viewing results. SymmDock, on the other hand, is a specialized algorithm for predicting cyclically symmetric homomultimers. It restricts its search to symmetric transformations, making it particularly efficient for predicting complexes with $C_{n}$ symmetry. The server requires users to input the asymmetric unit (monomer) and the symmetry order, and it generates predictions for the entire multimer. Both servers are available at http://bioinfo3d.cs.tau.ac.il, offering efficient and user-friendly solutions for molecular docking problems.