LoopWeaver

Server

This is where you'll find the link to the LoopWeaver server, once it is working

Data

Click Here for the test sets and LoopWeaver results from Holtby et. al. 2011
Each set of length X loops is seperated into "weaver_X.tar.bz2" for the original Weaver results, and "kic_weaver_X.tar.bz2" for the KIC refinments of the top LoopWeaver result. The file "weaver.pdb" contains all 500-1000 LoopWeaver predictions. The file "weaver_Dfire.pdb" contains the top 20 LoopWeaver predictions as ranked by their DFIRE energy potential. The first model in the one with the best energy value. "casp_models.tar.bz2" contains the PDB structure for all of the CASP8 and CASP9 targets, as well as the .dssp file containing the secondary structure predictions used to select loop targets. Each set of loop results also contains a "length_X.xray.list" file which lists the test loops used.

List File Format

The .list files follow the following format.

T0393   B : 107 - 113   HE

The first column is the CASP target identifier for the protein, the second column is the loop identifier (the first loop of a given length in a given target is "A", the second "B" and so on). The next two columns are the start and end residue numbers for the loop. These are the first/last residues within the loop, not their stems. In the above example, residues 106 and 114 are stems, while all the resiudes between them are the loop. A target can have many loop "A" as each loop length is part of an independent list. The final column indicates the secondary structure type of the stems. In the above example, residue 106 is a helix, and residue 114 is a strand. This information was not used by LoopWeaver, but may be useful for some tools (though they should be able to get this from the input file and not require a command line parameter).

Directory Structure Example

The directory "./T0393/len7B" contains the predictions for the second (loop B) length 7 loop identified in the CASP target T0393. The released structure for this target, loops included, will be in "./T0393/native.pdb" and the dssp structure classifications in "./T0393/native.dssp".