We present recent developments in efficiently maintaining the boundary and surface area of protein molecules as they undergo conformational changes. As the method that we devised k...
Background: Recent approaches for predicting the three-dimensional (3D) structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potentia...
: The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to...
Abstract. We extend the hyperdynamics method developed for lowdimensional energy-dominated systems, to simulate slow dynamics in more general atomistic systems. We show that a few ...
Motivation: In many proteins, helix-helix interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining associations between pro...
Anne E. Counterman Burba, Ursula Lehnert, Eric Z. ...