oGNM - Online service for Gaussian Network Model

PDB ID: with biological assembly (unit): No Yes
or upload a local file:

Chain ID: (e.g., A or AB, or leave blank for all chains)

Model No.: (for NMR solved structures)

No. of node(s) to represent a nucleotide: 1-node 3-node

Cutoff for amino acid nodes (Å):

Cutoff for nucleotide nodes (Å):

Spring constant for contact distance ≤ 4.0 Å:

Distance scaling factor for spring constant:

Salt bridge scaling factor for spring constant:

Environment GNM:
     using crystal contacts as environment: No Yes
     or using chain(s) as system (e.g., A or AB; remains are environment)
     or using the first residues as system (e.g., 100; remains are environment)

Molecular viewer: JsMol Jmol (fast response for big structures)

Email: (optional except for big PDB with 2000+ nodes)

Reference: Li,H., Chang,YY, Lee,JY, Bahar,I. and Yang,LW. (2017) DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Res., 45, W374-W380.

Contact:

The server is maintained by Dr. Hongchun Li in the Bahar Lab at the Department of Computational & Systems Biology at the University of Pittsburgh, School of Medicine, and sponsored by the NIH awards #5R01GM099738-04 and #5P41GM103712-03 and the funding #104-2113-M-007-019 from MOST to the Yang lab at the National Tsing Hua University, Taiwan.

For questions and comments please contact Hongchun Li.