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


October 17, 2016 - Alex Morriss-Andrews Transitions To Ann Arbor Medical Technology Company!
Congratulations to Alex, he has moved to a new position as a system engineer at NouMoDx Molecular. Good luck in the next stage of your career Alex.
October 5, 2016 - Nobel Prize In Chemistry - Molecular Machines
The Chemistry Nobel Prize goes to three European Scientists (though one now is at Northwestern) for their work on molecular machines. Cool stuff! (Link)
September 18, 2016 - UM Chemistry And Biophysics Departments Host Brooks 60th Symposium
Chemistry and Biophysics have organized a symposium recognizing Charlie's accomplishments during his first 60 years. Symposium speakers include: Cathy Royer (RPI), Ron Levy (Temple) and Ken Houk (UCLA).
September 5, 2016 - Welcome To Amanda Peiffer - Rotating From Chemical Biology Program
Amanda Peiffer will be rotating in the Brooks Group this semester. Amanda is from the Chemical Biology graduate program and is working on predicting the structures of VP16(aH1):Med25(AciD) and VP16:Med25(AciD) transcriptional activator complexes. Welcome Amanda!
September 1, 2016 - Welcome Garrett Meek As New Postdoc In The Brooks Group
Garrett Meek will join us from MSU as a postdoc. He will work on developing transferable coarse-grained models for protein-protein interactions.
July 29, 2016 - Charlie Elected President Of The Protein Society
Protein Society elections for new officers find Charlie as winning candidate for President. He will serve as President-elect (with Carol Post) for one year, followed by two years as President and one as Past President. Congratulations Charlie.
June 15, 2016 - Jonah Vilseck Joins Brooks Group As A Postdoc From Jorgensen Lab At Yale
Jonah is starting as a postdoc in the group with a focus on multi-site lambda dynamics and free energy methods. Welcome aboard Jonah.
June 5, 2016 - Welcome To Jessica Leuchter, Summer Rotation Student From Chemistry Graduate Program
Jessica will join us for the summer and will begin graduate studies in Chemistry in the fall. Jessica is working on constant pH molecular dynamics. Welcome to the group Jessica.
April 26, 2016 - Welcome New Grad Student Group Members Yanming Wang And Murchtricia Charles
The Brooks Group Welcomes our newest graduate student colleagues, Murchtricia Charles will be joining us from the Bioinformatics graduate program and Yanming Wang is coming to the group from the Chemistry program. Welcome!
April 12, 2016 - Kira Accepts Position With Merck
Congratulations to Kira and her new position with Merck. Kira will start her new position early this summer.
Funding from the following agencies: