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FORCASP • View topic - Preliminary results
Page 1 of 3

Preliminary results

PostPosted: Mon Aug 04, 2008 6:30 am
by mcguffin
Hi,

I've calculated some preliminary results for CASP8, based on 46 targets with released structures:



So far it looks as though the Zhang-Server will remain the best server in the TS category, by a significant margin. The only new server that is close in performance is the Phyre_de_novo server:

Cumulative results:
Significance tests:

Yang Zhang has also published results on his website:

http://zhang.bioinformatics.ku.edu/casp8/index.html

Liam

Re: Preliminary results

PostPosted: Thu Aug 07, 2008 6:26 am
by mcguffin
Results for 54 targets are now available.

Check here for updates:
http://www.reading.ac.uk/bioinf/CASP8/index.html

Re: Preliminary results

PostPosted: Thu Aug 28, 2008 11:36 am
by kevin_karplus
I like Zhang's assessment by TM_score and HB_score (perhaps because it puts my server second, right behind Zhang's). It seems that Zhang fixed the problem in CASP7 of bad models built on good CA traces, if he is now doing best at the Hbonds.

Re: Preliminary results

PostPosted: Wed Sep 03, 2008 2:46 am
by Guest
Whichever score we use, we need to assess the significance of the differences between methods based on common subsets. Slight differences in cumulative scores may be insignificant.

Based on the GDT-TS score, Zhang's server significantly out performs all others. However, there is no significant difference between the next 10 methods (p >= 0.01), so the rankings based on cumulative score may be due to chance.

For example, there are only two servers that significantly outperform the SAM-T08-server, which are the Zhang-Server and pro-sp3-TASSER. Follow the link below:


Re: Preliminary results

PostPosted: Wed Sep 03, 2008 2:52 am
by mcguffin
BTW the last post was me. I didn't realise you could post without logging in...

Liam McGuffin

Re: Preliminary results

PostPosted: Thu Sep 04, 2008 1:19 pm
by RAPTOR

Re: Preliminary results

PostPosted: Fri Sep 05, 2008 2:44 am
by guest

Re: Preliminary results

PostPosted: Fri Sep 05, 2008 9:52 am
by Guest

Re: Preliminary results

PostPosted: Sat Sep 06, 2008 5:25 am
by jlee
In the CASP7, to assess the quality of C_alpha trace, GDT-HA was used for both TBM and HA-TBM targets.
I would like to see the CASP8 assessors to use a even higher-accuracy measure such as GDT-TL (0.25, 0.5 1.0 2.0)
especially for HA-TBM tagets as done in the CAST6. Nowadays, protein model quality is improving steadily
especially for TBM targets, and CASP should ask/encourage predictors to devise more accurate modeling
globally (for FM targets) as well as locally (for TBM targets). I feel like 8A is too large a distance to be
meaningful even for FM targets (however, 8A gives us a complacent feeling of good protein modeling)

On the other hand, for the calculation of GDT scores, only positions of C_alpha atoms matter.
Since there are many more non-C_alpha atoms in protein models (CASP8 did not accept C_alpha only models),
CASP8 assessors should consider to include additional measures other than the HB score used in the CASP7.
Candidate measures include Chi_1 and Chi_12 for all/TBM targets.
One should also consider to use the HB score for all targets not restricted to TBM.

Just a thought....

Re: Preliminary results

PostPosted: Sat Sep 06, 2008 9:23 am
by test