Highlights•Biomolecular force fields (FFs) have progressed rapidly in the past five
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …

The protein folding problem was apparently solved recently by the advent of a deep learning
method for protein structure prediction called AlphaFold. However, this program is not able …

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural
dynamics of folded proteins and should be similarly applicable to disordered proteins and …

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 …

Protein structure and dynamics can be characterized on the atomistic level with both nuclear
magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here …

Many proteins can be partially or completely disordered under physiological conditions.
Structural characterization of these disordered states using experimental methods can be …

Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …

An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The
parametrization has been largely based on high-level ab initio calculations in order to keep …

The increasing availability of high-quality experimental data and first-principles calculations
creates opportunities for developing more accurate empirical force fields for simulation of …