The Protinfo dock fragment-based docking with dynamics (FDWD) server module predicts putative atomic level structures of protein/ligand complexes. Given a protein structure in PDB format, a ligand structure in mol, mol2, or PDB format, and (optionally) a binding site location on the protein structure, this module will determine five different possible protein/ligand complex structures. For each complex structure, the module reports a score that assesses the goodness-of-fit, or likelihood, that the given pose is a physically realistic. Binding sites may be given in terms of the coordinates of the estimated centroid of the ligand, or in terms of the residues surrounding the binding pocket. If no binding site is given the server will predict the location of the binding site. Results are available on a web page with a unique URL known only to the user.
New users may want to look at this short tutorial which includes an overview of how to use the server, and the format of the output.
Download the example protein and ligand data here.
Sample output is available here.