[BioPython] using Bio.PDB: fast way to get the maximum distance within a protein?

[Miguel Ortiz-Lombardía]

Hello,

You can align the protein coordinates against its principal axes of inertia.
This is very fast. One (free) program doing so is 'moleman2' from the
Uppsala Software Factory:

http://alpha2.bmc.uu.se/~gerard/usf/

HTH,


Miguel

2007/9/5, Peter <biopython at maubp.freeserve.co.uk>:
>
> Christian Meesters wrote:
> > Hi,
> >
> > Does anyone know a way to compute the maximum distance within a protein
> > (perhaps using Bio.PDB) without calculating distances of all atom
> > pairs?
>
> Are you thinking alpha-carbon to alpha-carbon distances, or using all
> atoms?
>
> > I'm hoping to be just too blind to see an easy solution here ...
>
> There should be some way to take advantage of the backbone links meaning
> lots of residues are constrained to be close to each other... Is it
> essential to get the largest pairwise distance, or would a local maximum
> do?
>
> You could probably do some clever sampling, say doing all pairwise
> combination of every third residue, and then for those furthest apart
> including all the local residues... just thinking out loud.
>
> Peter
>
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