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Enter the PDB ID (4-character) for structures available in the PDB

  
 

If you have a structure not deposited in PDB (a model obtained by homology modeling, or an assembly or a part of a PDB file), upload the structure coordinates in PDB format :

 
You can adjust the cutoff distance adopted in the GNM
for amino acid pairs:   Å            and
for nucleotide pairs:   Å
Preferred visualization engine: Jmol Chime

 

What does oGNM do?

oGNM calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM)1, a network model for representing biomolecules. (Figure). For retrieving pre-calculated PDB results go to the database iGNM (more details)2.

Note:

1. The submitted structure file should be in PDB format and contains 20-6200 NODEs (Ca atoms in proteins plus Phosphate atoms in DNA/RNA).

2. The uploaded input file should be less than 10 MB.

Features of oGNM :

1. Selectable cutoff distances for Ca-Ca in proteins (ranging from 6 to 20 Å) and P-P in nucleotides (ranging from 14 to 40 Å) . The cutoff of Ca-P is the arithmetic average of the two.

2. ALL of the Ca and P atoms in the uploaded structure will be taken as NODEs including both standard and non-standard amino acids and nucleotides.

3. The connectivity matrix is stored in a sparse format in the .kdat file where only non-zero contacts are recorded

4. BLZPACK3 is used as the current eigensolver.

5. Theoretically predicted B-factors (time average fluctuations over all modes) are calculated by the algorithm, PowerB.

6. The current output includes

  • the mobility profiles of residues corresponding to the 20 slowest modes of motion predicted by the GNM;

  • the average profile reuslting from the first 2 slowest modes;

  • the associated eigenvalues (21 of them, including the zero eigenvalue);

  • the predicted and experimental B-factors, and the correlation coefficient between the two sets of B-factors;

  • the spring constant (g) in units of kcal/mol.Å2

  • the cross-correlation between residue fluctuations, plotted as a correlation map (for structures containing less than 500 nodes).

  • the nodes included in the GNM analysis, summarized in the .ca file.

  • the coordination number of each node, listed in the .cont file

References:

1. "Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential" I. Bahar, A. R. Atilgan, and B. Erman Folding & Design 2, 173-181, 1997.

2. "iGNM: A Database of Protein Functional Motions Based on Gaussian Network Model." Lee Wei Yang, Xiong Liu, Christopher Jon Jursa, Mark Holliman, A.J. Rader, Hassan Karimi, Ivet Bahar.  Bioinformatics Jul 2005; 21: 2978 - 2987.

3.  "BLZPACK: Description and User’s Guide" Marques,O., TR/PA/95/30.CERFACS, Toulouse, France. 1995