The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

On the occasion of their fiftieth birthday, it is opportune to review the first half century of
Ramachandran plots. In the present review, some of the most relevant aspects of this fifty …

Rotamer libraries are used in protein structure determination, prediction, and design. The
backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles …

One of the major limitations of computational protein structure prediction is the deviation of
predicted models from their experimentally derived true, native structures. The limitations …

Distributions of the backbone dihedral angles of proteins have been studied for over 40
years. While many statistical analyses have been presented, only a handful of probability …

Recently, we developed a residue-specific force field (RSFF1) based on conformational free-
energy distributions of the 20 amino acid residues from a protein coil library. Most …

Traditional protein force fields use one set of parameters for most of the 20 amino acids
(AAs), allowing transferability of the parameters. However, a significant shortcoming is the …

Statistical potentials that embody torsion angle probability densities in databases of high‐
quality X‐ray protein structures supplement the incomplete structural information of …

The complex hydrophobic and hydrophilic milieus of membrane-associated proteins pose
experimental and theoretical challenges to their understanding. Here, we produce a …

Prediction of protein tertiary structures from amino acid sequence and understanding the
mechanisms of how proteins fold, collectively known as “the protein folding problem,” has …