Professor Simmerling’s research interests focus on the dynamic aspects of biomolecular
function, and how conformational changes affect important processes such as protein
folding, molecular recognition and enzymatic function. Specific applications of interest
are the role of dynamics in drug resistance and in recognition/repair of DNA damage.
Most of his recent publications on biological systems have been co-authored with experimental
collaborators, with a significant focus on integration of computation and experiment,
using simulations to interpret experimental observables and using experiments to validate
computational models. The biomolecular simulation field remains immature and thus
improvement of methods and models is also a focus of the Simmerling lab. Prof. Simmerling
has a long history of development and application of a variety of simulation methods,
and is currently one of six members of the leadership committee for the widely used
Amber molecular simulation program (with over 1000 site licenses). His lab has developed
force fields for proteins (cited over 3000 times), damaged DNA and small molecules.