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


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.
June 6, 2019 - Brooks Group Former, Anthony (Tony) Mustoe Accepts Faculty Position At Baylor School Of Medicine
Congratulations to Tony on his recruitment to Baylor School of Medicine where he will start as an Assistant Professor in 2019/20.
June 6, 2019 - Joe Yesselman Accepts Assistant Professor Position At University Nebraska, Lincoln!
Congratulations to former Brooks Group member Joe Yesselman. He will start as an Assistant Professor and the University of Nebraska, Lincoln this fall.
June 6, 2019 - Ryan, Yanming And Efrosini Present Their Work At PFC In St Louis
Brooks Group members participate in the Annual Protein Folding Consortium Meeting this weekend at Wash U, St Louis. Three days of scientific exchange and networking!
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 - Jonah Vilseck To Accepts Assistant Professorship At Indiana University School Of Medicine
Congratulations to Jonah, current Brooks Group Postdoc, for landing a faculty position at IU School of Medicine. Jonah will move to his new position in August. We will miss him!
June 5, 2019 - Efrosini Receives Rackham Travel Award To Attend 33rd Annual Symposium Of The Protein Society In Seattle
Congratulations to Efrosini in winning a Rackham Travel Award. Efrosini will present her research on pH-mediated chemical shifts in proteins and peptides at the meeting.
June 4, 2019 - Tricia Wins Travel Award And Speaking Spot At San Diego ACS
Congratulations to Tricia for winning a position to speak at the Women make COMP program as part of the San Diego ACS meeting in August. (Link)
June 3, 2019 - Efrosini Artikis' Paper To Appear In The Biophysical Journal
Congratulations to Efrosini on having her paper "Modeling pH Dependent NMR Chemical Shift Perturbations in Peptides" accepted in the Biophysical Journal. Onto proteins and pH!
May 8, 2019 - Congrats To Ryan For Hans Neurath Award From Protein Society
Hearty congratulations to Ryan Hayes for winning recognition of the Protein SOciety's Hans Neurath Outstanding Promise Award! Great job Ryan.
Funding from the following agencies: