Subject: NMA for proteins: http://www.bioinfo.no/tools/normalmodes

From: Nathalie Reuter <nathalie[at]ii.uib.no>
Date: Tue, 24 Aug 2004 18:23:27 +0200

We are pleased to announce the release of a new version of our web 
server for normal analysis of proteins, WEBnm@, available at 
http://www.bioinfo.no/tools/normalmodes. Go and try it !

The server is meant to provide users with simple and automated 
computation and analysis of low-frequency normal modes for proteins. The 
computation performed through our server should help the user understand 
whether your protein of interest undergoes large amplitude movements, 
and thus decide if it is worthwile performing a complete study with more 
thorough analysis. Analysis tools provided here have been described and 
successfully applied /(Reuter et al., Biophys.J., 2003)/. Normal modes 
calculations are performed using the MMTK package /(K. Hinsen, 
J.Comput.Chem., 2000)/. 

Analysis tools available so far are:
* deformation energies for low-frequency modes;
* calculation of normalized squared atomic displacements: results are 
provided either as raw data or as plots (PDF format);
* vector field representation: PNG image files or VMD state files;
* animations of the vibrations associated with the low-frequency modes: 
animated gif or dcd trajectory files.

We welcome comments and suggestions, and will surely take them into 
account in future versions.

-- 
Nathalie Reuter
Computational Biology Unit
BCCS/Univ. of Bergen
Thormohlensgt, 55
N-5008 Bergen
Phone: +47 55 58 40 40
Fax: +47 55 58 42 95