SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

Abstract

SuperLooper provides the first online interface for the automatic, quick and 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 Å, for loops up to six residues or <3 Å for loops shorter than 10 residues. Other suitable conformations may be selected and directly visualized on the web server from a top-50 list. For user guidance, 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. This allows the user to select the optimal membrane protein loop concerning its relative orientation to the lipid bilayer. The server is online since October 2007 and can be freely accessed at URL: http://bioinformatics.charite.de/superlooper/