DENM (Dissipative Electroelastic Network Model) is a software package designed to add dissipation to elastic network models (ENM) through electrostatic interactions of partial charges and can be used to describe both dynamic and static properties of proteins. The model combines the harmonic network of beads (ENM) with overdamped dynamics of the normal modes (Langevin dynamics).
Reference to published work:
- Dissipative electro-elastic network model of protein electrostatics, Physical Biology, 2012, 9(3), 036004
- Solvated dissipative electro-elastic network model of hydrated proteins, J. Chem. Phys., 2012, 137(16), 165101
This work was supported by the National Science Foundation (Molecular and Cellular Biosciences Division, Grant No. MCB-1157788 and by Chemical Theory, Models, and Computational Methods, CHE-1464810).
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