Paper Citing NAMD - Abstract
Das, Amit; Chakrabarti, J.; Ghosh, Mahua
Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation
BIOPHYSICAL JOURNAL, 104:1274-1284, MAR 19 2013
We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically.
