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:

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

Noncanonical Secondary Structure Stabilizes Mitochondrial tRNASer(UCN) by Reducing the Entropic Cost of Tertiary Folding

Anthony M. Mustoe, Xin Liu, Paul J. Lin, Hashim M. Al-Hashimi, Carol A. Fierke, Charles L. Brooks III: J. Am. Chem. Soc. (2015) 137, 3592-3599