CASP13 benchmark

  • Last update: 03 January 2019
  • File size: 133.14 MB
  • Version: 1
  • Downloaded: 12
  • Author: López-Blanco J.R. and Chacón P.
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#  --- KORP v1.22 release - January 3rd, 2019   ---  #
#  --- http://chaconlab.org/modeling/korp       ---  #
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> CASP modeling benchmarks
--------------------------
As a blind test requested by the referees, the predicted decoy models
for CASP 13 server protein modeling edition were downloaded from:
http://predictioncenter.org/download_area/CASP13/predictions_trimmed_to_domains/
on December 2018, and the target native structures from:
http://predictioncenter.org/download_area/CASP13/targets/casp13.targets.T-D.4public.tar.gz

All decoys were trimmed to single domains according to the CASP's
domain definition found at their website (e.g.
http://predictioncenter.org/casp13/domains_summary.cgi). Thus, for
a fair comparison, both native structures and the corresponding
decoys have the same number of atoms.

All targets without any decoy better than 0.5 GDT-TS score were removed.

The total number of original and ">0.5 GDT-TS scoring" targets and
structures are shown in the following table:

Benchmark         Targets*     Structures^
   id               [#]            [#]
------------------------------------------
casp13all'        32 / 27    12453 / 10698
------------------------------------------
* Original / >0.5 GDT-TS score.
^ Native structures included.
' All available decoys are included. Note that in this case, sel20 (stage 1)
and best150 (stage 2) benchmarks are not provided.

The CASP13DCall/ directory contains all the CASP decoys trimmed to domains.
Inside you will find all the native structures (e.g. T0957s1D2.pdb) and
all the decoys (e.g. T0957s1D2_s124m1.pdb). File name indicates,
respectively, the CASP target number (i.e. T0957s1), the domain (i.e.
D2), the server number (i.e. s124), and the model number (i.e. m1).
The input lists of cases for korpe are named casp13dcall_05.txt.

Note that a plain-text table ("TMall" file, e.g. casp13dcall_TMall05.txt)
with the C-alpha RMSDs, scores (TM, MS and GDT_TS), and the energies
computed using others potentials (ICOSA, RW+, GOAP, original ORDER_AVE,
VoroQ, and DOSP) can be found inside each benchmark sub-directory.


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CONTACT
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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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