AMBER Archive (2004)

Subject: Re: AMBER: Protein with maximum hydrogen bonds

From: pande.vineet_at_fc.up.pt
Date: Sat Nov 27 2004 - 08:13:58 CST

In my opinion»» it is in itself a matter of approximation for the
crystallographers to figure out intramolecular H-bonds, given an average
resolution structure...usually the H-bonds are judged based on distances
between heavy atoms...in this way, sometimes, for instance H-bonds directed by
Cysteine residues are underpredicted in X-tal structures..Although I am not
aware of any database where you could get a score based on intramol. H-bonds,
because it might be difficult to judge ALL the H-bonds in a protein...However
Disulphide bonds or metal bound complexes might be easy to search.....Why don´t
you look in WHATIF database...perhaps they have some way ..
Quoting anshul_at_imtech.res.in:

> Dear all the amber users,
> In my research project I need to do simulation on a protein with a lot of
> intramolecular hydrogen bonds (more the better). Does anyone know about a
> protein with maximum number of intramolecular hydrogen bonds in it; or is
> there any way by which I can get such a structure from PDB?
>
> Thanks in advance for any kind of help and suggestions.
>
> With best regards,
>
> Anshul Awasthi
> Bioinformatics Center
> Institute of Microbial Technology
> Chandigarh, India.
> Mobile +91-9872220352
>
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