Homology Modeling and CASP5 performance:
Homology Model Server
The server, developed by Grad.Student Jahnavi Prasad
and myself, can be reached directly at
Consensus
[1],
[2].
The main feature of the server is to identify regions of high
structural similarity (HSS) between a target sequence and a template.
If no template is given, the server will identify one for
comparative model targets.
The predicted HSS regions are typically less than 2.5 A RMSD from
the crystal structure, as estimated from the recent blind experiment
at the CASP5 meeting. The output of the server also includes an
optimal alignment between target and template. In a few weeks,
the server will be upgraded to output full 3-D PDB models
(instead of just the alignment).
Using the output of our server, we have also validated a (manual)
Comparative Modeling technique to predict accurate homology models.
To validate our methods, our performance on the recent CASP5 experiment
(where we submitted models for all targets) is summarized below.
We note that 215 research groups participated in CASP5, submitting
a total of 22909 models).
CASP5 (Asilomar, 2002):
CASP5/CAFASP3 results
Number of groups and servers contributing: 215
Number of models designated as Nr. 1: 7627
Summary of the performance of our group on the Comparative
Modeling category at CAFASP3 (servers) and CASP5 (manual), as
well as in the fold recognition (FR) and new fold (NF) category
is listed. Analysis includes ONLY models submitted as Nr. 1
prediction.
GROUP______________MEAN LENGTH________MEAN RMSD__NOTE
NAME_____CODE___TARGET__PREDICTED____(per Residue)
--------------------------------------------------------------------------------
CAFASP3__completely automatic structure prediction for CM targets.
Camacho__(#098)____158_______89__________2.4 A_______(1)
CASP5__manual (Top CM Predictors based on RMSD and LENGTH)
Camacho__(#099)____161______139__________4.8 A_______(2)
Bujnicki___(#020)____161______156__________5.2 A_______(2)
Fischer____(#427)____161______149__________5.7 A_______(2)
Baker_____(#002)____161______149__________5.9 A_______(2)
CASP5__manual (FR & NF category based on RMSD and Alignment LENGTH)
Camacho__(#099)____120________68_________11.7 A______(3)
Fischer____(#427)____120_______118_________15.2 A______(3)
Baker_____(#002)____120_______110_________13.0 A______(3)
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(1) Average is over the 44 comparative model (CM) targets of CASP5
that our server was able to automatically find a template in the PDB.
A total of 52 servers participated in this blind experiment, all
other servers predicted models with more than twice our mean RMSD.
(See, also, http://www.pdg.cnb.uam.es/CAFASP3Contacts_RESULTS/index.html)
(2) Average is over all 51 CM targets.
(3) Average is over all 30 FR & NF targets.
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