Re: [Apbs-users] Comparing proteins

[Nathan B. <ba...@bi...>]

Hello --
I would recommend that you look at the work of Rebecca Wade et al and Dennis
Livesay et al for these types of analyses.  The Wade group also has an
excellent software package (webPIPSA; http://pipsa.eml.org/) that can
perform comparisons like these for you.

Good luck,

Nathan

On Wed, Aug 5, 2009 at 6:57 AM, <se...@un...> wrote:

>
> Dear all,
>
> I would like to compare two small domains that bind DNA with different
> affinity. I have the pdb file for one domain and I know its binding
> region while for the other, since the sequence identity is very high,
> I build a model and, based on this, I would try to suggest why it
> binds DNA with higher affinity.
> Now my idea is to calculate the electrostatic potential for both
> domains and compare it in the binding region (a previous mail suggests
> the tools/mesh/multivalue to evaluate this).
> Since I'm not expert in this field I ask you if there is something
> different I could try and if there is some reference paper that deals
> with similar problems.
>
> Thanks for your help,
> Marco
>
>
>
> Dr.Marco Sette, Ph.D.
>
> Department of Chemical Sciences and Technology
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail:        se...@un...
> e-mail:        m7...@ya...
> Tel.:          +39-0672594424
> Fax:           +39-0672594328
>
>
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-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://bakergroup.wustl.edu/