Paper Citing NAMD - Abstract
Wu, Sangwook; Lee, Chang Jun; Pedersen, Lee G.
Analysis on long-range residue-residue communication using molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2896-2901, NOV 2014
We investigated the possibility of inter-residue communication of side chains in barstar, an 89 residue protein, using mutual information theory. The normalized mutual information (NMI) of the dihedral angles of the side chains was obtained from all-atom molecular dynamics simulations. The accumulated NMI from an explicit solvent equilibrated trajectory (600 ns) with free backbone exhibits a parabola-shaped distribution over the inter-residue distances (0-36 angstrom): smaller at the end regimes but larger in the middle regime. This analysis, plus several other measures, does not find unusual long-range communication for free backbone in explicit solvent simulations. Proteins 2014; 82:2896-2901. (c) 2014 Wiley Periodicals, Inc.
