The genetic diversity of HIV-1 represents a major challenge in vaccine development. In this
study, we establish a rationale for eliminating HIV-1–infected cells by targeting cellular …

An ongoing challenge in protein chemistry is to identify the underlying interaction energies
that capture protein dynamics. The traditional trade-off in biomolecular simulation between …

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-…

Defining the denatured state ensemble (DSE) and disordered proteins is essential to
understanding folding, chaperone action, degradation, and translocation. As compared with water-…

Predicting protein binding is a core problem of computational biophysics. That this objective
can be partly achieved with some amount of success using docking algorithms based on …

Single-molecule force spectroscopy methods, such as AFM and magnetic tweezers, have
proved extremely beneficial in elucidating folding pathways for soluble and membrane proteins…

In this work, we provide an interface developed to link the Molecular Modelling toolkit (MMTK)
with OpenMM in order to take advantage of the fast evaluation techniques of OpenMM. …

A standard wide field inverted microscope was converted to a spatially selective spectrally
resolved microscope through the addition of a polarizing beam splitter, a pair of polarizers, an …

Our group developed a force spectroscopy capability for use with our near-atomic level
Upside MD package, and applied it to the vertical and lateral pulling of bacteriorhodopsin (bR) …

In this study we will address the following issues: 1. Can we adapt our coarse-grained
folding algorithm, Upside, to predict binding? 2. What kinds of interactions are important for …