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Re: [modeller_usage] How Alignment Score is calculated.

On 04/09/2011 10:00 PM, Ashish Runthala wrote:

When pairwise alignment score calculated by MODELLER
is not parallel to the Model Accuracy. Then what is the benefit
Alignment Score holds for? Benn, will you please tell me the formula
for calculating Alignment Score for a pairwise alignment. What is the
matrix it uses for alignment and score computation. How it is
calculated.
The alignment score is simply the sum of residue-residue distances and gap penalties from tracing the path that dynamic programming finds through the alignment matrix.
In general, alignment scores are a poor predictor of model quality. I'm not aware of any claims to the contrary in the Modeller documentation. 

	Ben Webb, Modeller Caretaker
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