Dear friends,
I have some questions about the B value, generated from the Modeller along with the homology model. I am not sure how the temperature factor (Beta) is calculated (by MD simulation?). Since many homology modeling program didn't supply the information of B value, or just used it as a temporary space to fill up data, I am curious how serious the Modeller deals with it? Is it a proper data to estimate the flexibility of residues?
Any suggestions or comments are greatly appreicated.
Your sincerely, Xinhao Ye ---------- PhD candidate Department of Biological Systems Engineering, Virginia Tech Blacksburg, VA 24061 USA
On 4/28/11 3:01 AM, Sanger wrote: > I have some questions about the B value, generated from the Modeller > along with the homology model. I am not sure how the temperature factor > (Beta) is calculated (by MD simulation?).
It is simply the relative heavy violation of each residue: http://salilab.org/modeller/9.9/manual/node103.html#SECTION00103140000000000...
Ben Webb, Modeller Caretaker
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Sanger