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 …

The functional structure of proteins results from marginally stable folded conformations.
Reversible unfolding, irreversible denaturation, and deterioration can be caused by …

Many modern statistical applications involve inference for complex stochastic models, where
it is easy to simulate from the models, but impossible to calculate likelihoods. Approximate …

We introduce the new knowledge-based scoring function DSX that consists of distance-
dependent pair potentials, novel torsion angle potentials, and newly defined solvent …

Accurate energy functions are critical to macromolecular modeling and design. We describe
new tools for identifying inaccuracies in energy functions and guiding their improvement …

A 3D model of RNA structure can provide information about its function and regulation that is
not possible with just the sequence or secondary structure. Current models suffer from low …

Functional RNA molecules depend on three-dimensional (3D) structures to carry out their
tasks within the cell. Understanding how these molecules interact to carry out their biological …

To address the large gap between time scales that can be easily reached by molecular
simulations and those required to understand protein dynamics, we present a rapid self …

The inherent flexibility of intrinsically disordered proteins (IDPs) and multi-domain proteins
with intrinsically disordered regions (IDRs) presents challenges to structural analysis. These …

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 …