Subject: Cluster analysis: summary

From: [email-masked] (Felipe Pineda)
Date: Thu, 1 Feb 2001 14:56:53 +0000

Dear CCLers!

here is a summary of the responses i got to my posting and some personal
comments on a couple of them.

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My original enquiry:

i would be very grateful for any pointer to a software tool (utility in
commercial or academic s/w, standalone tool) which is able to perform such an
analysis on a set of conformers typically sampled by some FF MD protocol
(e.g.,simmulated annealing) and to build families of conformations displaying
similarity to each other with respect to an user defined structural feature
(backbone conformation, for example) to a given extent (some rmsd threshold)
specified by the user. i used some years ago an insightII macro called
family.bcl written by Don Mackay, 1991, which do this with the help of an
external program called also family:

(...)

but in the meantime there are maybe new, more efficient tools out there.
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The answers:

1. from David van der Spoel <[email-masked]>

The gromacs MD package has a clustering tool:

http://md.chem.rug.nl/~gmx

2. from Carlos Simmerling <[email-masked]>

moil-view is a free program for SGI that does cluster analysis.
there is a link to it from my page -> http://comp.chem.sunysb.edu/carlos

my comment:
we downloaded the unix distribution of moil-view v9.1 and used the program for
performing the cluster analysis. initially the only difficulty consisted in
getting our trajectories (available both in pdb and msi's sequential arc
format) in the formats supported by moil-view, i.e., DCD/PATH/AMBER/AMBER PBC).
we tried to do this by reading the pdb traj. files with VMD v1.6 for windows,
but, for some unknown reason, the generated binary DCD files could not be read
by moil-view. although latter was able to read and cluster some trajectories in
AMBER (crd) format also generated with VMD, other cdr files contained format
errors, so we had to do the corresponding conversion (pdb -> cdr) with a small
piece of fortran code. moil-view does the job fine and its functionality is
very similar to that of the old insight macro i mentioned above.

3. from Sérgio Emanuel Galembeck <[email-masked]>

In my lab we use XCluster software to make
cluster analysis after conformational search. Results
are very good and agree with experimental information.
This software is part of MacroModel suite.

4. from Peter Shenkin <[email-masked]>:

MacroModel, from Schrodinger, Inc., includes XCluster, which is
described in J. Comp. Chem., v15, #8, 899-916 (1994).

See www.schrodinger.com for some more details (including the
manual)

5. from Doree F Sitkoff <[email-masked]>

I've used the program NMRCLUST, freely available at
 http://neon.chem.le.ac.uk/nmrclust/protocol.html

5. from Jodi Shaulsky <[email-masked]>

5.1.
If you have InsightII the Analysis module allows you to create and
manipulate cluster graphs from which families can be defined. This
is done using the Trajectory/Construct_Graph with the 'Cluster_Graph'
button 'on'

5.2.
Did you look at the Family command under the Trajectory pulldown. It looks
like you can do everything that the script would do using command Family.
It will create an assembly of the comformers that meet the criteria you
set. This assembly can then be writen out to a file.
I looked around for the macro called family but was not able to locate it.

my comment:
after generating the clustergraph (i.e. the rmsd matrix the clustering is based
on) i was playing around for a while with the Analysys/Trajectory/Family pull
down, as advised. unfortunately, i was not able to perform the cluster
analysis, but only to generate a single family of conformers at each time based
on different criteria. i am convinced that it should be possible to write a
simple insight macro using the (new) family command, but that was not really
the solution i was looking for.

Thanks a lot to everybody who responded.

Best regards

felipe

-- 
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* Felipe Pineda,PhD                                                  *
* Institut fuer Molekulare Biotechnologie                            *
* AG Theoretische Biophysik                                          *
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