Classic benchmarks

  • Last update: 28 November 2018
  • File size: 141.68 MB
  • Version: 1
  • Downloaded: 9
  • Author: López-Blanco J.R. and Chacón P.
0.0/5 rating (0 votes)
######################################################
#  --- KORP v1.22 release - November 26th, 2018 ---  #
#  --- http://chaconlab.org/modeling/korp       ---  #
######################################################


> 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              [#]        [#]
----------------------------------
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.


-------
CONTACT
-------

Please, feel free to contact with us!
(suggestions or bug reports are welcome)

Jose Ramon Lopez-Blanco (PhD.)
This email address is being protected from spambots. You need JavaScript enabled to view it.

Pablo Chacon (PhD.)
This email address is being protected from spambots. You need JavaScript enabled to view it.