VMD-L Mailing List

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Feb 19 2009 - 15:14:45 CST

This link would be interesting to you.
http://webclu.bio.wzw.tum.de/stride/

One way I can think about scoring is :
Since in a perfect helix, there is a well defined angle (a_0), and
dihedral (b_0) for each point, a simple function could look like :
f(h) = Exp{-(a-a_0)^2/c_1} * Exp{-(b-b_0)^2/c_2}
, where a, b are instant value of angle, and dihedral. However, it
might be a little tricky here about the way to calculate angle and
dihedral.

Hope this helps.
Bin

On Feb 19, 2009, at 10:27 AM, Suman Chakrabarty wrote:

> I shall be interested to know if you (and others) have found any
> solution to this. I don't have a protein system though. I have a
> simple linear polymer chain, which can have helical segments. I would
> like to quantify the helical content in the chain.
>
> Which would be right way to proceed here? Thanks for any help.
>
>
> Regards,
> Suman.
>
>
> On Fri, Jan 16, 2009 at 12:39 AM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>> Hi, All:
>>
>> Is there a way to score a peptide chain according to its helicity,
>> say to
>> define a function f(h), and f(h) = 1 for perfect alpha helix, and
>> f(h) = 0
>> for random coil?
>>
>> I probably can hack the STRIDE code and get a start on this, but
>> still, I
>> want to hear your ideas. ;-)
>>
>> Any suggestion is appreciated.
>>
>> Thanks a lot.
>>
>> Bin

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