Hi Jacob,
> I am looking at ~20 unique crystal structures of the same protein in somewhat
> different conformations, although not radically different, and would like to
> order them somehow to gain an understanding of how the protein can move. Is
> there software that does this somewhat automatically?
There are so many different things that you may want to look at, that I
doubt you'll find a single program doing all of them automatically. You
could, for example, examine (after removal of global rotations-translations)
- The variance-covariance matrix
- Graphs of the RMSD of the CA-CA distances
- Do PCA and analyse the motion in terms of principal components (in
Cartesian space), or calculate the 20x20 matrix of rmsds and use that to
do cluster analysis with R.
- Do PCA-based cluster analysis and select representative structures for
each cluster (Cartesian space).
- Do dihedral PCA and cluster analysis in dihedral space.
- Calculate a (hypothetical) average structure and the corresponding
RMSFs to identify mobile regions (compare with observed Bs) ...
... and the list goes on. I think it boils down to one thing: what is the
question ?
My twocents,
Nicholas
--
Dr Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
