Gaussian Network Model
The Gaussian network model (GNM) is a representation of a biological macromolecule as an elastic mass-and-spring network to study, understand, and characterize mechanical aspects of its long-scale dynamics. The model has a wide range of applications from small proteins such as enzymes composed of a single domain, to large macromolecular assemblies such as a ribosome or a viral capsid.
The Gaussian network model is a minimalist, coarse-grained approach to study biological molecules. In the model, proteins are represented by nodes corresponding to alpha carbons of the amino acid residues. Similarly, DNA and RNA structures are represented with one to three nodes for each nucleotide. The model uses the harmonic approximation to model interactions, i.e. the spatial interactions between nodes (amino acids or nucleotides) are modeled with a uniform harmonic spring. This coarse-grained representation makes the calculations computationally inexpensive.
At molecular level, many biological phenomena, such as catalytic activity of an enzyme, occur within the range of nano- to millisecond timescales. All atom simulation techniques, such as molecular dynamics, rarely reach microsecond trajectory length, depending on the size of the system and accessible computational resources. Normal mode analysis in the context of GNM or elastic network (EN) models, in general, provides insights on the longer-scale functional behaviors of macromolecules. Here, the model captures native state functional motions of a biomolecule in the cost of atomic detail. The inference obtained from this model is complementary to atomic detail simulation techniques.
Another model for protein dynamics based on elastic mass-and-spring networks is the Anisotropic Network Model.
Other articles related to "gaussian network model, network models":
... HingeProt An algorithm for protein hinge prediction using elastic network models http//www.prc.boun.edu.tr/appserv/prc/hingeprot/, or http//bioinfo3d.c ...
Famous quotes containing the words model and/or network:
“The Battle of Waterloo is a work of art with tension and drama with its unceasing change from hope to fear and back again, change which suddenly dissolves into a moment of extreme catastrophe, a model tragedy because the fate of Europe was determined within this individual fate.”
—Stefan Zweig (18811942)
“How have I been able to live so long outside Nature without identifying myself with it? Everything lives, moves, everything corresponds; the magnetic rays, emanating either from myself or from others, cross the limitless chain of created things unimpeded; it is a transparent network that covers the world, and its slender threads communicate themselves by degrees to the planets and stars. Captive now upon earth, I commune with the chorus of the stars who share in my joys and sorrows.”
—Gérard De Nerval (18081855)