Paper Citing NAMD - Abstract
Krishnan, Marimuthu; Smith, Jeremy C.
Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4124-4133, APR 12 2012
An analytical approach is developed for reconstructing site-specific methyl-bearing protein side-chain conformational energy surfaces from NMR methyl axis order parameters (O-axis(2)). Application of an enhanced sampling algorithm (adaptive biasing force) to molecular dynamics simulation of a protein, calcium-bound calmodulin, reveals a nonlinear correlation between O-axis(2) and the populations of rotamer states of protein side-chains, permitting the rotamer populations to be extracted directly from O-axis(2). The analytical approach yields side-chain conformational distributions that are in excellent agreement with those obtained from the enhanced-sampling MD results.
