Re: [Apbs-users] absolute binding energy

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

Hello --

Absolute binding free energy calculations are extremely challenging.  In
your text below, it sounds like you are outlining a MM/PBSA or similar
approach which is one way to address this problem.  However, it is unlikely
that MM/PBSA will give you quantitatively-accurate absolute binding free
energies; this method works best for relative free energies.

-- Nathan

On Mon, Nov 16, 2009 at 8:38 AM, Tiago Lopes Gomes <
tia...@ir...> wrote:

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>> hello,
>> a beginner's question.
>> I have some Kd derived from itc (isothermal titration calorimetry)
>> experiments on some protein-peptide complexes.
>> I would like to calculate some binding energies with apbs, and compare it
>> with experiments. I understand that apbs doesn't calculate absolute binding
>> energies, and that this could be a tricky question. How could i do this
>> (calculating SASA with be necessary i guess).
>> Meaning, what "percentage" of the absolute binding energy does apbs
>> calculate, and which tutorial should i use.
>> Could I incorporate other software and "sum" the
>> other contributions (normal mode analysis, entropic contributions..) to the
>> apbs ones?
>> I guess that following the overall binding cycle in the tutorial isn't the
>> final calculation.
>>
>> thank you
>>
>> Tiago
>>
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-- 
Nathan Baker (ba...@bi...)
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/