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Dear all,
I have been learning a bit of docking and as nowadays I see some
programs try to incorporate some protein flexibility in the algorithms,
flexibility they extract (partially ?) from the atom B-factors, that led me
to consider how important might be to refine due TLS tensors.
As I said before, I saw some cases in which the incorporation of TLS
tensors to the model reduced much the R-factors (as a matter of fact, since
when I started using TLS tensors, I never saw a case where *both* my
R_factors did not improve at using TLS tensors, although in some cases the
improvement was small). When we do not use TLS tensors, I think refinement
programs "tend" to incorporate the "disorder" associated with rigid body
movement into individual B-factors.
In the case where the active site is completely located into one single
subunit and there is a "good" rigid body movement, such that the inclusion
of a TLS tensor (for the whole subunit) leads to a better model (lowering
significantly the R-factors) and, consequently, in the pdb file the atoms
present much lower B-factors (correspnding to the residual "flexibility"),
it must be much better to use, then, this residual B_factors yet they
repesent a "local" "from one to other atom" relative flexibility, for doking
purposes, right ?
Anyway, I still do not know how much the flexibility expressed by the
B-factors impacts the results of docking. I would like to hear comments
about this or would thank some literature on the subject. After all, I
wonder how much I should care the B-factor refinement for a protein I refine
which will subsequently used for docking andthe consequences of this.
Of course, the discussion gets more complex when you have an active site
which is formed by more subunits or are better refined with parts of it
belonging to different "rigid" groups.
***********************************************************************
Prof. Jorge Iulek, Ph. D.
Protein Purification and 3D Structure Determination Group
State University of Ponta Grossa
Telephone: ++ 55 - 42 - 3220-3062
Fax: ++ 55 - 42 - 3220-3262
[EMAIL PROTECTED]
[EMAIL PROTECTED]
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