Welcome to the Brooks Group Website!

Research in the group of Charles L. Brooks III in the Department of Chemistry and Biophysics Program at the University of Michigan is focused on the application of statistical mechanics, quantum chemistry and computational methods to chemically and physically oriented problems in biology. Current research interests include:

• multi-scale modeling applied to dynamics and assembly of complex biological assemblies, e.g., viruses, ribosome, myosin
• development of constant pH molecular dynamics with applications to pH dependent conformational changes: folding, unfolding and aggregation of proteins and nucleic acids
• RNA structure, function and folding processes using all atom and coarse-grained models
• free energy based methods for inhibitor screening and optimization, including lambda-dynamics, ligand docking, protein stability and continuum based free energy approximations
• coupling between protein motion and enzyme catalysis in DHFR, AdK, DNA polymerases, including QM/MM investigations of enzyme catalysis
• coarse-grained modeling of molecular machines: ribosome, viruses, helicases
• development of new polarizable force fields for proteins, lipids and small molecules
• protein folding using all atom and simplified off lattice models, including unfolded states of proteins
• protein structure prediction, ab initio folding, homology modeling

In addition, we are oversee the development and support of the CHARMM molecular mechanics and modeling software. Our efforts in software development focus on new methods for the problems noted above and high performance computing on large parallel and distributed supercomputers, including accelerated molecular dynamics using GPUs.