[gmx-users] Refolding modeling

Ansuman Lahiri albmbg at caluniv.ac.in
Thu Mar 17 12:18:25 CET 2005

This is an interesting problem. However, it seems it is too general
at this point.

To be able to use MD, one must have a structure of the protein.
And then one must also have an idea about the properties of the
ligand, since some ligand will barely perturb the structure and
some (like denaturants, if they can be called ligands) will 
completely unfold the protein. Ab initio prediction of structure
is one possibility but probably not that accurate.

I am interested to know about other opinions.

Best regards,


> Hello gmx-users,
> Suppose, we have a protein that may change its folding upon ligand
> binding. We have not possible template for this process from other
> homologues proteins and dont know what kind of ligand may be here.
> What we can do in this situation?
> May be, first step is in identification of flexible and rigid regions
in the
> protein by means of such kind of programs as DomainFinder. An then use
> some force influence on such sites by some technics from Molecular
> Dynamics? And if yes, what this technics is?
> Thank you very much for your attention and suggestions.
> -- 
> Best regards,
> D. Egorov,
> Ural State Medical Academy.
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Ansuman Lahiri
Department of Biophysics, Molecular Biology & Genetics
University of Calcutta
92, APC Road, Kolkata 700009, India

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