Showcase

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

Please visit Google Scholar for a list of citations of the CHARMM program.

Recent research listed below highlights the diverse functionality of CHARMM:

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; Read More

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; Read More

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; Read More

Anisotropy of B-DNA Groove Bending: Ning Ma, Arjan van der Vaart: J. Am. Chem. Soc. (2016) 138, 9951-9958; Read More

Efficient implementation of constant pH molecular dynamics on modern graphics processors: Evan J. Arthur, Charles L. Brooks: J. Comp. Chem. (2016) 37, 2171-2180; Read More

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; Read More

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; Read More

Transition path theory analysis of c-Src kinase activation: Yilin Meng, Diwakar Shukla, Vijay S. Pande, Benoit Roux: PNAS (2016) 113, 9193-9198; Read More

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; Read More

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; Read More

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; Read More

Modeling Protein–Micelle Systems in Implicit Water: Rodney E. Versace, Themis Lazaridis: J. Phys. Chem. B (2015) 119, 8037-8047; Read More

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; Read More

Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics: Min Xu, Andrea Unzue, Jing Dong, Dimitrios Spiliotopoulos, Cristina Nevado, Amedeo Caflisch: J. Med. Chem. (2015) ASAP; Read More

Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins: Nathan Desdouits, Michael Nilges, Arnaud Blondel: J. Mol. Graph. Model. (2015) 55, 13-24; Read More

Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL: Xiaorong Liu, Alex Beugelsdijk, Jianhan Chen: Biophys. J. (2015) 109, 1049-1057; Read More

Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin: Maksym Solovlov and Markus Meuwly: J. Chem. Phys. 143, 105103 (2015); Read More