DynOmics Portal 1.0 - Dynamics of Structural Proteome and Beyond

What is the DynOmics ENM server?
The DynOmics ENM server computes biomolecular systems dynamics for user-uploaded structural coordinates or PDB identifiers, by integrating two widely used elastic network models (ENMs) – the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM). Unique features include the consideration of environment, the prediction of potential functional sites and reconstruction of all-atom conformers from deformed coarse-grained structures. For more information see Theory and Tutorial.

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)

Advanced options:

Model No.: (for NMR solved structures)

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

Cutoff distance (for GNM analysis only) (Å):

Cutoff for nucleotide nodes (Å):

Spring constant scaling factor for contact distance ≤ 4.0 Å: (sequential neighbors)

Distance scaling exponent (p) for spring constant:

Salt bridge scaling factor for spring constant:

Considering Environment:

ENM in the presence of an environment:
     in the presence of membrane: No Yes
     or in the presence of crystal neighbors: No Yes
     or using chains/residues as system
     (range selection, e.g., AB or 1-100 or A:1- or A:1-100;B:100-200)

      Selection of additional atoms (other than amino acids and nucleotides) as environment:

segname: chain: resname: resid: atom:

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

Email: (optional, except for PDB files with > 2,000 residues)

Load examples:

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.