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.
1. The submitted structure file should be in PDB format.
2. The uploaded input file should be less than 10 MB.
3. Normal mode results are returned for structures containing 20-12000 NODEs
For 1-node per nucleotide model: NODEs = Ca atoms in proteins + Phosphor atoms in DNA/RNA
For 3-node per nucleotide model: NODEs = Ca atoms in proteins + Phosphor/C4*(in the sugar)/C2(in the base) atoms in DNA/RNA
4. Time average fluctuation results are returned for structures containing 20-6400 NODEs. You have to initiate the calculation manually after the normal mode
results are obtained.
Features of oGNM :
1. oGNM provides direct computation of dynamics for proteins' biologically functional unit by switching the radial selection from 'PDB Files' to 'Biological Unit File'. Note that oGNM takes the entire PDB file (all the MODEL entries) as a whole and assumes it an integral complex if you check 'Biological Unit File'. For instance, you DO NOT want to check 'Biological Unit File' if you submit an NMR structure containing multiple models. By checking 'PDB File', oGNM will only compute the normal modes for the first model in an NMR structure.
2. Selectable cutoff distances for Ca-Ca in proteins (ranging from 6 to 20 Å) and P-P in nucleotides (ranging from 9 to 40 Å for 1-node per nucleotide model; 6.5 to 40 Å for 3-node per nucleotide model) . The cutoff of Ca-P is the arithmetic average of the two.
3. ALL of the Ca and nucleotide atoms (P or P/C4*/C2) in the uploaded structure will be taken as NODEs including both standard and non-standard amino acids and nucleotides.
4. The connectivity matrix is stored in a sparse format in the .kdat file where only non-zero contacts are recorded
5. BLZPACK3 is used as the current eigensolver.
6. Theoretically predicted B-factors (time average fluctuations over all modes) are calculated by the algorithm, PowerB.
7. The current output includes
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
This page is maintained by Lee-Wei Yang . Please let us know if you encounter any problem while using this website hence a better assistantship to describe the dynamics of your proteins.