Re: software/algorithm to cluster protein conformations

From: Nicholas M Glykos (
Date: Fri Apr 30 2010 - 04:40:02 CDT

> I would like to cluster different conformations of a protein focusing on
> certain residues and their side chains. Is there any available
> softwares/algorithms that would perform this?

If you assign to the atoms you are interested-in a distinct SEGID,
say L, then you can use

# carma -v -w -col -cov -eigen -dpca 5 3 298 -segid L protein.dcd protein.psf

for performing a PCA-based clustering in dihedral space (which ignores
side chains), or better,

# carma -v -w -col -cov -eigen -proj 5 3 298 -segid L -atmid HEAVY protein.dcd protein.psf

for performing a PCA-based clustering (using all heavy atoms) in Cartesian
space. If you'd rather be safe than sorry, you can use something like

# crossDCD protein.psf protein.dcd protein.dcd 200 " -segid L -atmid HEAVY "

to prepare a square matrix with all frame-to-frame rmsds between the
selected atoms (all heavy atoms of SEGID L) which you can then use with a
statistics program (like R) for cluster analysis. Both carma and
the crossDCD script are available from


          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,

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