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ELASTIC NETWORK MODEL
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THE MODEL (Tirion, 1996): 
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All atoms less than "cutoff" Angstroms away from each other 
are linked by springs of same strength.

Additional asumptions, with respect to Tirion's original work:
Cartesian coordinates, atoms of same size. 
Possibly: of same masses (otherwise masses are read in coordinate file).

Main Result:
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Low-frequency normal modes obtained with this model
are very close to those obtained with standard
empirical descriptions at the atomic level (like with CHARMM).

Main advantages over standard approaches:
No preliminary energy-minimization required (minimum Energy=0,
by definition). Can be quick (with one-atom-per-aminoacid-residue).

To see what it can do:
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Go at:
http://igs-server.cnrs-mrs.fr/elnemo/

PROGRAMS: 
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To compile them:
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make pdbmat
make diagstd

What they do:
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pdbmat:  
       This is the "Tirion" matrix builder:
       from a PDB coordinate file, or a "x, y, z, mass" one,
       yields a "Tirion" matrix, in the following format:
       i, j, non-zero-ij-element.

       Reads commands from a file called "pdbmat.dat".
       A first run yields a "pdbmat.dat_run" exemple file (default commands).

diagstd: 
       Diagonalize "Tirion" matrix.

       Expects "pdbmat.sdijf" or "pdbmat.sdijb" matrix files.
       Creates "pdbmat.eigenfacs" (eigenvectors, written in "CERFACS" format),
       For large matrices, in order to obtain low-frequency eigenvectors, 
       use DIAGRTB, a separate program.

A few references:
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M.M. Tirion (1996):
"Large amplitude elastic motions in proteins from
a single-parameter, atomic analysis",
Phys. Rev. letters vol.77(9), p1905-1908.

I. Bahar, A.R., Atilgan, B. Erman, B (1997):
"Direct evaluation of thermal fluctuations in proteins
using a single-parameter harmonic potential",
Folding & Design vol.2, p173-181.

K. Hinsen (1998):
"Analysis of domain motions by approximate normal mode calculations",
Proteins vol.33, p417-429.

F. Tama, Y.H. Sanejouand (2001):
"Conformational change of proteins arising 
from normal modes calculations"
Protein Engineering vol.14, p1-6.

M. Delarue , Y.H. Sanejouand (2002): 
"Simplified normal mode analysis of conformational transitions in
DNA-dependant polymerases: the Elastic Network Model", 
J. Mol. Biol. vol.320, p1011-1024. 

