It is well-established that dynamics are central to protein function; their importance is
implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of …

The use of residual dipolar couplings (RDCs) in the analysis of biomolecular structure and
dynamics has expanded rapidly since its potential as a source of structural information on …

Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force
field is required. The Amber ff99SB force field improved protein secondary structure balance …

The development and validation of new peptide dihedral parameters are reported for the
OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1 …

While the quality of the current CHARMM22/CMAP additive force field for proteins has been
demonstrated in a large number of applications, limitations in the model with respect to the …

Development of the AMOEBA (atomic multipole optimized energetics for biomolecular
simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes …

Refinement is a process that involves bringing into agreement the structural model,
available prior knowledge and experimental data. To achieve this, the refinement procedure …

NMR chemical shifts in proteins depend strongly on local structure. The program TALOS
establishes an empirical relation between 13 C, 15 N and 1 H chemical shifts and backbone …