[Biojava-l] Constructing Backbone of Protein

[Mohammed AlQuraishi]

In general it's not possible to accurately reconstruct a protein's backbone
strictly from phi/psi angles--you'd need the bond lengths and bond angles
(especially important) to have an accurate reconstruction. It is however
possible to get an approximate reconstruction, particularly for short
protein fragments, if you use "standard" values for bond lengths and angles,
such as the ones here:

http://scripts.iucr.org/cgi-bin/paper?li0061

I don't know if biojava has any methods specific for this purpose, but the
link below contains a description of how to reconstruct the coordinates if
you have the dihedral angles (and bond lengths and angles) that doesn't
require more functionality than simple 3D transforms:

https://lists.sdsc.edu/pipermail/pdb-l/2002-December/000326.html

Hope this helps,
Mohammed

---
Mohammed AlQuraishi
McAdams and Shapiro Labs
Stanford University

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
Sent: Friday, July 18, 2008 7:05 AM
To: Richard Holland
Cc: biojava-1 mailing list
Subject: Re: [Biojava-l] Constructing Backbone of Protein

Hi Richard,

This email actually managed to find its way through to the list back  
in May...
http://www.biojava.org/pipermail/biojava-l/2008-May/006211.html

Andreas


On 17 Jul 2008, at 20:15, Richard Holland wrote:

> Not sure. Andreas Prlic should know. Andreas....?
>
> 2008/5/13 Armita Sheari <armita_sh at yahoo.com>:
>> Hi everyone,
>>
>> I need to write a program that can construct  the backbone of the  
>> protein
>> from  its sequence and the relevant phi and psi angles.  I want to  
>> know if
>> there is a class or method that can help me to calculate the  
>> coordinates
>> form phi and psi angles!
>>
>> thanks,
>> ArmitaSh
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

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