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