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.


March 3, 2015 - Afra's Paper "Membrane Environment Modulates The PKa Values Of Transmembrane Helices" Accepted In J Phys Chem B
Congratulations Afra on paper number 9 of the year!
February 23, 2015 - Congratulations To Tony For Paper Number Eight Of The Year Accepted In JACS
Tony's paper on mitochondrial RNA folding and stability examined with TOPRNA will appear shortly in JACS. Thanks to Tony for a great job, and our collaborators, Carol Fierke, Hashim Al-Hashimi, Paul Lin and Xin Liu.
February 15, 2015 - Bon Voyage To Charlie As He Leaves For A Short Sabbatical At The Weizmann Institute In Israel
Charlie will spend 1-2 months visiting the Weizmann Institute in Rehovot, Israel. He has received a prestigious Visiting Professorship during his visit.
February 10, 2015 - Another Brooks Group Paper With Mauricio Carrillo-Tripp Accepted In J. Struct. Biol.
Congratulations to Mauricio on publication of his paper on "Protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps". Exploring viral capsid protein-protien interfaces.
February 6, 2015 - Congratulations To Kira And Garrett For Paper Number Five For 2015!
Kira's and Garrett's paper "Biasing Potential Replica Exchange Multi-Site Lambda-Dynamics for Efficient Free Energy Calculations" is accepted for publication in JCTC. Nice job!
February 3, 2015 - Elena, Garrett And Alex Get JACS Paper Accepted!
Paper number four for the year "pH-dependent Transient Conformational States Control Optical Properties of Cyan Fluorescent Protein" ia accepted in JACS. Congratulations Elena, Garrett and Alex.
January 28, 2015 - Congratulations To Xinqiang For Passing His Candidacy Exam!
Xinqiang passed his candidacy exam in Bioinformatics. He's now a PhD candidate! Great job.
January 15, 2015 - Shanshan Has Third Paper Of 2015 - PCAlign In Press In BMC Bioinformatics
Congratulations Shanshan.
January 7, 2015 - Congratulations To Fox And Tuli Mukhopadhyay On Getting The Second Paper Of The Year Accepted - In PNAS
Our paper "Residue level resolution of alphavirus envelope protein interactions in pH dependent fusion" was accepted for publication in PNAS. Great job Fox and Tuli!
January 6, 2015 - First Paper Of The Year Accepted In JMB!
The paper by Logan, Alex and Sean - Multiscale Modeling of a Conditionally Disordered pH-Sensing Chaperone - will appear in JMB shortly. This paper outlines a complete multi-scale approach for examining structure-function relationships in the conditionally disordered HdeA protein chaperone. Congratulations guys!
Funding from the following agencies: