In the Madhusudhan paper, the cutoff was at least 70% for a SO of 3.5 A. What number does that correspond to in the salign output?

For the quality score, is there an objective number that I can use for every alignment to see whether it is good or not?

Lastly, for "iterative salign," is it recommended to run the regular version first or just jump straight to using the iterative salign? The Madhusudhan paper seems to forgo the use of iterative salign if the alignment is 70% at a SO of 3.5, but if there were enough computing resources, would it be wise to run iterative salign without running the regular version first?

I know it's a lot of questions, but thanks in advance for answering them.

--Brian

From: Modeller Caretaker <modeller-care@salilab.org>
To: Brian Tsui <btsui17@yahoo.com>
Cc: "modeller_usage@salilab.org" <modeller_usage@salilab.org>
Sent: Tuesday, July 26, 2011 10:05 AM
Subject: Re: [modeller_usage] Good Quality Score

On 7/25/11 10:10 PM, Brian Tsui wrote:
> In the output for salign, there is a raw quality score, a percentage
> quality score, and many other values. What value should I focus on to
> make sure that I have a good alignment? Is there a cutoff that I should
> use? If so, are there references that I could cite?

For a structural alignment, there is an objective measure of the "best" alignment - that which maximizes the percentage of residues within the cutoff distance. This is the "quality score", which is roughly similar to the GDT_TS score; see Protein Eng Des Sel 22, 569-574, 2009. Modeller includes an "iterative structural alignment" method which maximizes this score.

For a sequence alignment, you have a tougher job - it depends what you want to use the alignment for. For comparative modeling, one approach is to score the quality of models built using that alignment. See Nucleic Acids Res 31, 3982-3992, 2003.

Ben Webb, Modeller Caretaker
-- modeller-care@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage