Dear Sir Benn, You are absolutely correct about CA-CA distance deviations, but when you choose 2 templates with CA-CA distances 5, 6 angstroms, then it will give you a better model as compared to 5, 10 angstroms set.

Secondly, precise sequence alignment is always neccessary, but correctly aligned incorrect templates will still give bad models and probably shifted residues as was the general case till CASP5 and CASP6.

Iterative Structural alignment also forces mathematical satisfaction of alignment, with no justification of biological significance of optimally placed gaps. So we still need better alignments.

Now I request your expert reply against these views.

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

Message: 2 Date: Thu, 21 Jul 2011 08:36:05 -0700 From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] Multiple Sequence Alignment vs Single Alignment To: Daniel Li leeyuhang@yahoo.com Cc: modeller_usage@salilab.org Message-ID: 4E284765.1020106@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 7/21/11 12:16 AM, Daniel Li wrote: > From reading it seems as if multiple templates should usually generate > better scores but running 3 trials of 600 with different sets of > templates for different proteins I still get better results from my > single template models. So is there something I have to manipulate with > the scripts and parameters?

Multiple templates generally do give better models, but they are more sensitive to alignment errors - the templates have to be quite well aligned with each other, otherwise they will present conflicting information (e.g. one template says that a given CA-CA distance is 5 angstroms, and another 10 angstroms) which is difficult to satisfy.

Ben Webb, Modeller Caretaker