WLoop

The WLoop Homology Modeling Server

The WLoop Homology Modeling Server is a tool to predict protein loop backbone structures from their sequences and their flank backbone structures.
Atomic coordinates of the alpha carbons of the regular secondary structures flanking the loop must be provided.
It functions upon a knowledge based principle.
Presently WLoop can accept attempting to build loops of size three to twelve.
However, we strongly advise that models of more than eight residues are very difficult to predict from a databank, and therefore results must be considered with extreme care. Some incorrections can occur for such sizes.

To use this service, you MUST provide:

A PDB formatted file with the missing parts to fulfill.
The sequence of the complete protein. It must be lowercase for the known parts, uppercase for the loops to build.
The sequence specified in lowercase MUST match that of the input PDB file.
The secondary structure of the protein, expressed as a sequence of H,E, C. H stands for helix, E for extended, other characters are assimilated to coil.
This information is used to select a prototype to build the loop. Results may depend on its definition, in particular, incorrect secondary structure may lead to select incorrect loop template, or to not build it. Loops for which the secondary structure of the three residues flanking both sides do not correspond to EEE or HHH will not be considered. You may force one of these for modelling purpose, but notice it can be hazardous.

Note: Only one chain can be processed at a time.

Additional help can be found here
Sample input can be found here

Successive loop banks and server facilities have been created by Jérôme Wojcik, Jean-Marc Kwasigroch, Ludovic Autin, Nicolas Renault, Nicolas Mandard, David Boëns, Pierre Tufféry and Jacques Chomilier.

REFERENCES

A global taxonomy of loops in globular proteins. J.-M. Kwasigroch, J. Chomilier, J.-P. Mornon. J. Mol. Biol. (1996) 259 855-872

New efficient statistical sequence dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J. Wojcik, J.-P. Mornon, J. Chomilier. J. Mol. Biol. (1999) 289 1469-1490

The WLoop Homology Modeling Server

Select a file (.pdb)

Chains to consider (ex: A,D):

or enter a PDB Id (ex: 1tim, 1timA)

Note: if you specify both an upload and a PDB Id, the upload will not be considered.

Here is a tool to visualize the sequence and secondary structure of a PDB file.

Maximal loop length:

Amino acid sequence of the complete protein :

Secondary structure of the complete protein :

REFERENCES