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Re: [modeller_usage] Model assessment - GA341



The cited work (Melo et.al., 2002) discusses the derivation of the statistical potentials used in the composite score. Please use "B. John,  A. Sali.  Comparative Protein Structure Modeling by Iterative Alignment, Model Building, and Model Assessment. Nucleic Acids Research 31, 3982-3992, 2003" to understand how the GA341 score works. 

FYI:

GA341 = 1 - [ cos(sequence_identity) ]^(compactness+sequence_identity)/exp(z-score)
 

Sequence identity is the fraction of positions with identical residues in the target- 
template alignment. Structural compactness is the ratio between the sum of the 
standard volumes of the amino acid residues in the protein and the volume of the 
sphere with the diameter equal to the largest dimension of the model. The Z-score 
is calculated for the combined statistical potential energy of a model, using the 
mean and standard deviation of the 200 random sequences with the same composi- 
tion and structure as the model (Melo et al., 2002). The combined statistical poten- 
tial energy of a model is the sum of the solvent accessibility terms for all Cβ atoms 
and distance-dependent terms for all pairs of Cα and Cβ atoms. The solvent acces- 
sibility term for a Cβ atom depends on its residue type and the number of other Cβ 
atoms within 10Å; the non-bonded terms depend on the atom and residue types 
spanning the distance, the distance itself, and the number of residues separating 
the distance-spanning atoms in sequence. These potential terms reflect the statisti- 
cal preferences observed in 760 non-redundant proteins of known structure. The 
GA341 scoring function was evolved by a genetic algorithm that explored many 
combinations of a variety of mathematical functions and model features, to opti- 
mize the discrimination between good and bad models in a training set of models. 
The GA341 score ranges from 0 for models that tend to have an incorrect fold to 1 
for models that tend to be comparable to at least low-resolution x-ray structures. 
GA341 scores greater than 0.7 indicate a correct fold with more than 35% of the 
backbone atoms superposable to better than 3.5Å. 

Eswar.

---
Eswar Narayanan
University of California - San Francisco


On Jul 8, 2006, at 7:45 AM, Cassiano wrote:

Hi all,

I have some questions about the model.asses_ga341. In the manual on-line 
is described that it uses the "percentage sequence identity between the 
template and the model as a parameter". But, in the cited work (Melo et 
al, 2002) i don't see this relation with sequence identity. My questions:
- How Modeller treat the sequence identity in the context of the cited work?
- If the identity between my target and templates is very low, how the 
quality of the model is affected? (and what you recommend to use to 
assess the quality)

Thanks,
Cassiano Carromeu.
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