Protinfo Dock (FDWD) - fragment-based docking with dynamics server module

Protinfo Dock (FDWD)

Horst JA, Laurenzi A, Bernard B, Samudrala R. Computational multitarget drug discovery. Polypharmacology 263-301, 2012.
Bernard B, Samudrala R. A generalized knowledge-based discriminatory function for biomolecular interactions. Proteins: Structure, Function, and Bioinformatics 76: 115-128, 2009.
Jenwitheesuk E, Horst JA, Rivas K, Van Voorhis WC, Samudrala R. Novel paradigms for drug discovery: Computational multitarget screening. Trends in Pharmacological Sciences 29: 62-71, 2008.

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.

Protein:
Please upload a PDB file of the protein.

Ligand:
Please upload a mol, mol2, sdf, or PDB file of the ligand.

Binding site:
Please give a comma delimited list of the indexes of the residues defining the binding pocket.
OR
Binding site:
Please upload a PDB file of a template ligand within the binding site.
OR
Binding site:
Please give the comma-delimited XYZ coordinates of the estimated position of the centroid of the binding site with respect to the protein structure.
OR
Binding site: Do not give any information about the binding site, and let the FDWD server predict the binding site location.

Binding site radius:Å
Please enter a number between 10 and 30 for the radius (in Angstroms) of the search space sphere about the binding site centroid. The server will search for binding site poses within this radius. The default value is 10.

Email(optional):
Please provide an e-mail if you would like notification when results are available.

Download the example protein and ligand data here.

Sample output is available here.

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