Frequently Asked Questions
1) How does iELM work?
Please see the about page or read our paper (coming soon)
2) What do the scores mean?
SCORE - the overall score for the iELM algorithm produced using the SVMlight algorithm
Domain Score - a score of similarity to a known annotated SLiM-binding domain
Motif Score - a score based on relative local conservation of the SLiM - see SLiMSearch 2.0 for more details
Pepsite Score - a score based on a PSSM score of the peptide results from Pepsite - see PepSite website for more details
3) Why are some PepSite structures missing?
A problem with the present form of Pepsite is that if many prolines in sequences it goes into a infinite loop. No results are produced for these inputs and therefore we do not have a predicted structure. This problem is being verified at the moment.
4) How do i view Pepsite predictions?
Click the link underneath the Pepsite title. This will download the Pepsite prediction for the peptide. Save this as a .pdb file locally and open within a structural visualization software, such as Pymol, Jmol or Chimera. Open this downloaded file together with the PDB file mentioned in Pepsite column. e.g for 1qqgB.DTANNPLBK, download 1qqg.