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Protein Structure Modelling  

DePristo et al. Cα-trace models

Here you can download the models used to analyze the RAPPER conformational search algorithm and evaluate sidechain modelling on near-native backbones, as described in DePristo et al., "Discrete restraint-based protein modeling and the Cα-trace problem".

These files has been tarred together and compressed with bzip2. Under unix you can expand the archive with:

bzip2 -d FILE.tar.bz2
tar xvf FILE.tar

A list of all targets can be downloaded here. You can also get all of the PDB structures, cleaned up with REDUCE.

We have generated ensembles of Cα and sidechain centroid models conformations with RAPPER, for each target in the above list.

Mainchain-only models

Model typeFile
under 0.25 Å Cα restraintsmainchain-only-ca0.25.tar.bz2
under 0.5 Å Cα restraintsmainchain-only-ca0.5.tar.bz2
under 0.75 Å Cα restraintsmainchain-only-ca0.75.tar.bz2
under 1 Å Cα restraintsmainchain-only-ca1.tar.bz2
under 2 Å Cα restraintsmainchain-only-ca2.tar.bz2
under 3 Å Cα restraintsmainchain-only-ca3.tar.bz2
under 4 Å Cα restraintsmainchain-only-ca4.tar.bz2
under 5 Å Cα restraintsmainchain-only-ca5.tar.bz2

All-atom models

Model typeFile
under 1 Å Cα and 1 Å sidechain centroid restraintsall-atom-centroid1.tar.bz2
under 1 Å Cα and 2 Å sidechain centroid restraintsall-atom-centroid2.tar.bz2
under 1 Å Cα and 3 Å sidechain centroid restraintsall-atom-centroid3.tar.bz2
under 1 Å Cα and 4 Å sidechain centroid restraintsall-atom-centroid4.tar.bz2
under 1 Å Cα and 5 Å sidechain centroid restraintsall-atom-centroid5.tar.bz2

Each archive file uncompresses to a subdirectory. In this subdirectory there is another subdirectory for each target, containing the models for that TARGET. There are many files in each target subdirectory:

benchmark.dat
Summary information about the conformations generated by RAPPER.
models.dat
Information about the each of the conformations generated by RAPPER.
build.out.gz
Output log of the RAPPER program. Contains a lot of detailed information about the progress and operation of RAPPER. Gzipped to conserve space.
native.pdb
The crystal structure PDB of target protein structure without the surrounding structure.
looptest.pdb and looptest-best.pdb
These files contain the RAPPER generated conformations, one conformation per MODEL in the PDB file. looptest-best.pdb is the conformation with lowest global mainchain RMSD to the crystal structure. The remarks preceding each model include information about the conformation.
scwrl-models.pdb
For the all-atom models, this file contains the ensemble of structures in looptest.pdb but with sidechains reassigned with the program SCWRL.

© 2001-2006 The RAPPER Team 
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