The rise and fall of artificial neural networks is well documented in the scientific literature of
both computer science and computational chemistry. Yet almost two decades later, we are …

Since Anfinsen demonstrated that the information encoded in a protein's amino acid
sequence determines its structure in 1973, solving the protein structure prediction problem …

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

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 …

The parametrization and validation of the OPLS3 force field for small molecules and proteins
are reported. Enhancements with respect to the previous version (OPLS2. 1) include the …

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 …

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

A fundamental challenge in biological research is achieving an atomic-level description and
mechanistic understanding of the function of biomolecules. Techniques for biomolecular …

Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …