Dear MODELLERS, 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.
Thanks Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
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
participants (2)
-
Ashish Runthala -
Modeller Caretaker