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


July 2, 2018 - Welcome To New Postdoc TJ Paul
The Brooks Lab welcomes new group member TJ, who joins us from the University of Miami. Welcome TJ.
May 30, 2018 - Welcome To Candidate Sara Tweedy
Great news, though expected, our fellow Brooks group member and MSTP graduate student Sara Tweedy successfully passed her candidacy exam in the Program in Chemical Biology today. Congratulations Sara!
April 10, 2018 - Outstanding Talks By Brooks Lab Undergrads
Congratulations to Daniel Evans, Noor SoHail and Milo Hartsoe who gave outstanding talks at our group meeting today. Noor explored benchmark comparisons between TI and MSLD and Milo and Daniel discussed the nature and quality of ancestral sequence reconstructions on model parameters. Great material!
February 26, 2018 - Congratulations Xinqiang Ding On Rackham Fellowship
Graduate student Xinqiang Ding won a prestigious Rackham Pre-doctoral Fellowship. Great going Xinqiang!
September 27, 2017 - Applications Programmer Needed In Brooks Group
The Brooks Group is interested in hiring an applications programmer to work with the CHARMM development team to implement CHARMM functionality on high performance computing platforms, GPUs and parallel architectures. (Link)
August 18, 2017 - Xinqiang, Ryan And Jonah All Present At DC ACS Meeting
Xinqiang, Ryan and Jonah will each present talks on their current research at the ACS National meeting in DC next week on M, T and W. See you in the audience!
August 18, 2017 - Elena Laricheva Accepts Faculty Position, Congratulations!
Former Brooks group postdoc Elena Laricheva accepted a faculty position as an Assistant Professor of Chemistry at Utah Valley University. Big congrats from Brooks group! (Link)
August 10, 2017 - Congratulations To Xinqiang, He's Married!
Xinqiang returned from vacation as married person, knock me over with a feather. Congratulations!!!
August 3, 2017 - Tricia Wins Support On Bioinformatics Training Grant
Congrats to Tricia for being selected to be supported on the Bioinformatics Training Grant for a second year!
July 23, 2017 - Congratulations To Tricia On Her Recent Nuptials
The Brooks group congratulates Tricia on her wedding. Enjoy your post wedding holidays.
Funding from the following agencies: