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# --- KORP v1.22 release - November 26th, 2018 --- #
# --- http://chaconlab.org/modeling/korp --- #
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> Classic modeling benchmarks
-----------------------------
The classic Rosetta and I-Tasser protein modeling benchmarks were
downloaded from http://fons.bakerlab.org/rosetta_decoys_62proteins.tgz
and https://zhanglab.ccmb.med.umich.edu/decoys, respectively.
Benchmark Targets Structures
id [#] [#]
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rosetta41 41 4599
itasser56 56 24650
The rosetta41/ directory contains well-scoring Rosetta protein decoys
(e.g. 1scj_073.pdb) and their native crystal structures (e.g.
1scj.pdb). Natives were refined in Rosetta to produce 20 relaxed
decoys (e.g. 1scj_rx_15.pdb) relieving clashes and, in some cases,
repacking rotamers. See the README in the author's downloaded file
for more information (not provided here).
The itasser56/ directory contains the decoys for the 56 non-homologous
small proteins of the Decoy Set II. This decoy set is a non-rudundant
subset of the I-TASSER decoys (Set-I). The raw decoys were first
generated by I-TASSER ab initio simulation, which were then
structurally refined by GROMACS4.0 using OPLS-AA force field with the
purpose of removing steric clashes and refining torsion angles. Each
set includes 300-500 decoys, which was used to test the atomic
potentials, including RW and RW+ potentials, see: J Zhang and Y Zhang,
A Distance-Dependent Atomic Potential Derived from Random-Walk Ideal
Chain Reference State for Protein Fold Selection and Structure
Prediction. PLoS One, vol 5, e15386 (2010).
Note that a plain-text table ("TMall" file, e.g. rosetta41_TMall.txt) with
the C-alpha RMSDs, scores (TM, MS and GDT_TS), and the energies
computed using others potentials (ICOSA, RW+, GOAP, ORDER_AVE, VoroQ,
DOSP, and CSF) can be found inside each benchmark sub-directory.
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CONTACT
-------
Please, feel free to contact with us!
(suggestions or bug reports are welcome)
Jose Ramon Lopez-Blanco (PhD.)
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Pablo Chacon (PhD.)
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