THIS WEBSERVICE IS TEMPORARILY UNAVAILABLE FOR MAINTENANCE
FINDSITE-metal is an extension of FINDSITE that predicts metal-binding sites, residues and binding metal preferences from evolutionarily related templates detected by threading. Furthermore, it employs machine learning to improve the prediction accuracy particularly against low-to-moderate quality protein structures. Thus, crystal structures as well as protein models can be used as the targets.
- This web service is freely available to all academic users and not-for-profit institutions.
- Commercial users wishing an evaluation copy should contact email@example.com .
- Commercial users may license the FINDSITE-metal software after completing the license agreement and sending it to firstname.lastname@example.org Download the license agreement.
If you use FINDSITE-metal, please cite the following paper:
- Brylinski M and Skolnick J (2011) FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal binding site prediction at the proteome level. Proteins: Structure, Function, and Bioinformatics. 79(3):735-751.
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. Estimated TM-score must be in the range of 0.0-1.0.
Download the source code and install FINDSITE-metal locally
Take a look at FINDSITE-metal 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. The list of proteins and associated metal binding ions is available here. We tested FINDSITE-metal using different quality target structures:
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.
Q: How to estimate the TM-score for my protein model?
A: This is described in FINDSITE-metal manual, see Appendix A.
This service was created and is maintained by Michal Brylinski