CASP benchmark

  • Last update: 28 November 2018
  • File size: 887.65 MB
  • Version: 1
  • Downloaded: 11
  • Author: López-Blanco J.R. and Chacón P.
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#  --- KORP v1.22 release - November 26th, 2018 ---  #
#  --- http://chaconlab.org/modeling/korp       ---  #
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> CASP modeling benchmarks
--------------------------
The predicted decoy models for CASP 10, 11, and 12 server protein
modeling editions were obtained from, for example,
http://predictioncenter.org/download_area/CASP12/server_predictions/.

Three CASP benchmarks per modeling edition are provided:
  all     --> All available decoys
  sel20   --> Stage 1
  best150 --> Stage 2

All decoys were trimmed to single domains according to the CASP's
domain definition found at their website (e.g.
http://predictioncenter.org/casp12/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               [#]            [#]
------------------------------------------
casp10all         99 / 78    34122 / 25092
casp11all         81 / 58    26656 / 17507
casp12all         44 / 32    15139 / 10056
casp10dcbest150   99 / 78    11729 /  9232
casp11dcbest150   81 / 55    11423 /  7680
casp12dcbest150   44 / 28     5849 /  3745
casp10dcsel20     99 / 73     1834 /  1333
casp11dcsel20     81 / 46     1610 /   914
casp12dcsel20     44 / 23      889 /   470
------------------------------------------
* Original / >0.5 GDT-TS score.
^ Native structure included.

The input files with all the decoy names required for korpe multi-run
are provided. They are named <benchmark_id>.txt. For example, 3DR200.txt
for 3DRobot or casp12dcsel20_05.txt for CASP12-sel20 without targets
without decoys better than 0.5 GDT-TS score.

The CASPxxDCyy/ directories contain the corresponding CASP decoys
trimmed to domains for the sel20 and best150 sets, where the "xx"
indicates the CASP edition, i.e. 10, 11, or 12, and "yy" the benchmark
sets, i.e. all, sel20, or best150.

Inside you will find all the native structures (e.g. T0676D1.pdb) and
all the decoys (e.g. T0676D1_s114m3.pdb). File name indicates,
respectively, the CASP target number (i.e. T0676), the domain (i.e.
D1), the server number (i.e. s114), and the model number (i.e. m3).
The input lists of cases for korpe are named caspXXdcYY_05.txt.

Note that a plain-text table ("TMall" file, e.g. casp12dcsel20_TMall05.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.)
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Pablo Chacon (PhD.)
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