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 30, 2020 - Tricia Presents At ACS Panel Biochemistry And AI
We are all excited to hear Brooks group member Tricia participate in an ACS panel on Biochemistry and Artificial Intelligence.
September 25, 2020 - Congratulations To Assistant Research Scientist Ryan Hayes
We are excited to announce that Ryan has moved to an Assistant Research Scientist position within the Department of Chemistry. Congratulations Ryan.
September 15, 2020 - Welcome To Dalia Hassan - Chemistry Rotation Student
The Brooks Group sends out a big welcome to incoming graduate student Dalia Hassan who is doing her fall rotation in the group. Welcome Dalia!
August 21, 2020 - Welcome To Our New Postdoc Xiaorong Liu
Dr Liu joins us from Jianhan Chen's group at U Mass, Amherst. Big welcome to Xiaorong.
August 17, 2020 - Congratulations To TJ And Rachel On The Birth Of Lily
TJ and Rachel expanded their family by one last night. Daughter Lily and Rachel are doing well. Congratulations to you all!
August 17, 2020 - Welcome To Lily Paul - Born To Rachel And TJ
The Brooks Group welcomes Ms Lily Paul, recently joining us from birth! TJ and family are happy and well!
August 10, 2020 - Au Revoir To Furyal From The Brooks Lab
We say (officially) goodbye to REU coworker Furyal Ahmed this week. Furyal gave an excellent presentation at today's group meeting. She has worked closely with our COVID-19 team and made excellent progress! Thanks Furyal.
June 9, 2020 - Congratulations To Efrosini Aka Dr Artikis
Efrosini gave a beautiful thesis presentation in the successful defense of her thesis. Congratulations! Efrosini is heading of to a postdoc with Byron Caughey's lab at the NIH in Montana.
December 10, 2019 - Congratulations To Former Lab Member Xinqiang Ding For Paper In Nature Communications
Machine learning and protein sequences! Deciphering protein evolution and fitness landscapes with latent space models (Link)
December 6, 2019 - Congratulations To Tricia - DEI Scientific Spotlight
Check out the great story about Tricia! (Link)
Funding from the following agencies: