Showcase

CHARMM is used by many groups around the world for exciting research in biology, chemistry, physics, material science and related disciplines.

Recent research listed below highlights the diverse functionality of CHARMM:

	pyCHARMM: Embedding CHARMM Functionality in a Python Framework Joshua Buckner, Xiarong Liu, Arghya Chakravorty, Yujin Wu, Luis Cervantes, Thanh Lai, Charles L. Brooks III: Journal of Chemical Theory and Computation 2023 19 (12), 3752-3762
	All-atom adaptively biased path optimization of Src kinase conformational inactivation: Switched electrostatic network in the concerted motion of αC helix and the activation loop Heng Wu, He Huang, Carol B. Post: J. Chem. Phys. (2020) 153 175101
	Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site Simone Conti, Kevin J. Kaczorowski, Ge Song, Katelyn Porter, Raiees Andrabi, Dennis R. Burton, Arup K. Chakraborty, Martin Karplus: PNAS (2021) 118, e2018338118
	The αβTCR mechanosensor exploits dynamic ectodomain allostery to optimize its ligand recognition site Wonmuk Hwang, Robert J. Mallis, Matthew J. Lang, Ellis L. Reinherz: PNAS (2020) 117, 21336-21345
	Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms Xinqiang Ding, Yujin Wu, Yanming Wang, Jonah Z. Vilseck, Charles L. Brooks III: JCTC (2020), 16, 3910-3919
	Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion Yalun Yu, Andreas Krämer, Richard M. Venable, Andrew C. Simmonett, Alexander D. MacKerell Jr., Jeffrey Klauda, Richard W. Pastor, Bernard R. Brooks: JCTC (2021), 17, 1562-1580
	Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics E. Prabhu Raman, Thomas J. Paul, Ryan L. Hayes, Charles L. Brooks III: JCTC (2020), 16, 7895-7914
	M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus Hedieh Torabifard, Afra Panahi, Charles L. Brooks III: PNAS (2020) 117, e1913385117
	Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA Yandong Huang, Wei Chen, David L. Dotson, Oliver Beckstein, Jana Shen: Nature Communications (2016), 7, 12940
	CHARMM36m: an improved force field for folded and intrinsically disordered proteins Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L. de Groot, Helmut Grubmüller, Alexander D. MacKerell Jr.: Nature Methods (2016), 14, 71-73
	Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects Daniel Roston, Qiang Cui: J. Am. Chem. Soc. (2016) 138, 11946-11957
	Anisotropy of B-DNA Groove Bending Ning Ma, Arjan van der Vaart: J. Am. Chem. Soc. (2016) 138, 9951-9958
	Efficient implementation of constant pH molecular dynamics on modern graphics processors Evan J. Arthur, Charles L. Brooks: J. Comp. Chem. (2016) 37, 2171-2180
	Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael Feig: eLife (2016) 5, e19274
	Structural effects of modified ribonucleotides and magnesium in transfer RNAs You Xu, Alexander D. MacKerell Jr., Lennart Nilsson: Bioorganic & Medicinal Chemistry (2016) 24, 4826-4834
	Transition path theory analysis of c-Src kinase activation Yilin Meng, Diwakar Shukla, Vijay S. Pande, Benoit Roux: PNAS (2016) 113, 9193-9198
	Computational Study of Gleevec and G6G Reveals Molecular Determinants of Kinase Inhibitor Selectivity Yen-Lin Lin, Yilin Meng, Lei Huang, Benoit Roux: J. Am. Chem. Soc. (2014) 136, 14753-14762
	Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion Xiancheng Zeng, Suchetana Mukhopadhyay, Charles L. Brooks III: Proc. Natl. Acad. Sci. USA (2015) 112, 2034-2039
	Mechanism of the Association between Na+ Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters Sebastian Stolzenberg, Matthias Quick, Chunfeng Zhao, Kamil Gotfryd, George Khelashvili, Ulrik Gether, Claus J. Loland, Jonathan A. Javitch, Sergei Noskov, Harel Weinstein, Lei Shi: J. Biol. Chem. (2015) 290, 13992-14003
	Modeling Protein–Micelle Systems in Implicit Water Rodney E. Versace, Themis Lazaridis: J. Phys. Chem. B (2015) 119, 8037-8047