SuperLooper -- Loop Structure Predictor
What you can do:
Predict the spatial conformation of loops in membrane proteins.
Highlights:
- SuperLooper is an online interface for the automatic, interactive search and placement of loops in proteins (LIP).
- A database containing half a billion segments of water-soluble proteins with lengths up to 35 residues can be screened for candidate loops.
- A specified database containing 180,000 membrane loops in proteins (LIMP) can be searched, alternatively.
- Loop candidates are scored based on sequence criteria and the root mean square deviation (RMSD) of the stem atoms.
- Searching LIP, the average global RMSD of the respective top-ranked loops to the original loops is benchmarked to be <2 A, for loops up to six residues or <3 A for loops shorter than 10 residues.
- Other suitable conformations may be selected and directly visualized on the web server from a top-50 list.
- The sequence homology between the template and the original sequence, proline or glycine exchanges or close contacts between a loop candidate and the remainder of the protein are denoted.
- For membrane proteins, the expansions of the lipid bilayer are automatically modeled using the TMDET algorithm.
Keywords:
- membrane protein
- protein loop
- spatial conformation
- tertiary structure
Literature & Tutorials:
This record last updated: 08-13-2009