FINDSITE

FINDSITE is a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.

NOTE:

• This web service is freely available to all academic users and not-for-profit institutions.
• Commercial users wishing an evaluation copy should contact skolnick@gatech.edu .
• Commercial users may license the FINDSITE software after completing the license agreement and sending it to skolnick@gatech.edu Download the license agreement.

If you use FINDSITE, please cite the following papers:

• Brylinski M and Skolnick J (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci USA 105:129-34 PDF
• Skolnick J and Brylinski M (2009) FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform 10:378-91 PDF

FINDSITE uses the following compound libraries:

Submit your target structure to our server

NOTE: The server accepts only single protein chains 40-400 residues in length. Only the ATOM section is parsed, non-standard residues are removed. Missing heavy atoms are added. PROSPECTOR_3, SP3 and Sparks2 threading algorithms are used to identify evolutionarily related templates. You can upload either the crystal structure or the predicted model of your target.

Download the source code and install FINDSITE locally

Take a look at FINDSITE benchmarks

Benchmark results provided below were obtained using weakly homologous (<35% sequence identity to the target) templates identified by three threading algorithms: SP3, Sparks2 and PROSPECTOR_3. We tested FINDSITE using different quality target structures:

FAQ

Q: How long does it take before my results are ready?
A: The simulation time depends on several factors: the length of the protein, the number of identified templates and the workload on our computer cluster. Typically, the results should be ready within 1-2 days. We are working to reduce the turn around time.

Q: How long will my results be kept on the server?
A: The results will be kept on the server for one month.

This service was created and is maintained by Michal Brylinski