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.

News


September 19, 2019 - Congratulations To Yanming On Publication Of JPC Lett Paper On Allostery And Electrostatics
Yanming's paper exploring the role of electrostatics in allostery and a novel HREX method are described in his latest accepted paper in JPC Lett (just accepted)!
September 19, 2019 - Congrats To Sara And Troy For JPC Paper On Radical-coupled Electron Transfer Mechanism!
Exciting new paper from Sara and Troy as part of Narayan/ZImmerman collaboration, see https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.9b08178
August 29, 2019 - Goodbye To Colleagues And Co-workers Juanrong Zhang And Parveen Sood
Today we say farewell to Juanrong, who came as a visitor from China for 6 months, and Parveen, who worked with us for a bit over a year. Juanrong will continue her Ph.D. studies at Tsinghua University. Parveen is moving on to a new stage of his career, hoping to embrace data science.
August 29, 2019 - Yanming, Tricia And Jonah Present At ACS Fall Symposium In San Diego
Yanming and Jonah presented excellent posters on their work on GPU accelerated Generalized Born models (Yanming) and MSLD bench marking on BACE I. Tricia and Jonah presented exceptional talks on ML -MATCH and Gibbs Sampler MSLD. Great job from all!
August 24, 2019 - Congrats To Our Leader!
Charlie wins National ACS Award for Computers in Chemistry and Pharmaceutical Sciences (Link)
July 3, 2019 - Amanda, Efrosini, Ryan And TJ Present Work At 33rd Annual Symposium Of The Protein Society In Seattle, WA
Excellent poster presentations from Amanda, TJ, Ryan and Efrosini in Seattle. We all had a great time exploring Protein Science and Seattle.
June 28, 2019 - Congratulations To Ryan For Winning Protein Society's Hans Neurath Travel Award To Attend And Present At The 33rd Annual Protein Society Symposium
Great job Ryan!
June 21, 2019 - Hedi Presents Her Research Findings On PH/ligand-dependent Stability Of G-alpha Proteins At Proteins GRC In New Hampshire
Great interactions and great poster presentation by Hedi at the Proteins GRC in Holderness, NH. Way to go Hedi!
June 6, 2019 - Xinqiang Ding Starts Postdoctoral Studies In Zhang Lab At MIT
Congratulations to Xinqiang and his move postdoctoral studies in the Bin Zhang lab in the Department of Chemistry at MIT. (Link)
June 6, 2019 - Sara Tweedy To Present Her Work At The Annual MD/PhD National Student Conference In Colorado
Sara will present her work on "Exploring Flavin Dynamics in Biocatalyst TropB with Theory and Molecular Modeling" at Colorado conference of MD/PhD students in mid-July.
Funding from the following agencies: