The John Chodera Lab: Publications


Visit PubMed for a full listing of John Chodera’s journal articles

Pubmed is an online index of biomedical articles maintained by the U.S. National Library of Medicine and the National Institutes of Health.

A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation. Emily F. Ruff, Joseph M. Muretta, Andrew Thompson, Eric W. Lake, Soreen Cyphers, Steven K. Albanese, Sonya M. Hanson, Julie M. Behr, David D. Thomas, John D. Chodera, and Nicholas M. Levinson. eLife, in press. [DOI] [bioRxiv]

Quantitative self-assembly prediction yields targeted nanomedicines. Yosi Shamay, Janki Shah, Mehtap Işık, Aviram Mizrachi, Josef Leibold, Darjus F. Tschaharganeh, Daniel Roxbury, Januka Budhathoki-Uprety, Karla Nawaly, James L. Sugarman, Emily Baut, Michelle R. Neiman, Megan Dacek, Kripa S. Ganesh, Darren C. Johnson, Ramya Sridharan, Karen L. Chu, Vinagolu K. Rajasekhar, Scott W. Lowe, John D. Chodera, and Daniel A. Heller. Nature Materials, in press. [DOI] [PDF] [Supporting Info] [nano-drugbank]

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculationsKevin Hauser, Christopher Negron, Steven K. Albanese, Soumya Ray, Thomas Steinbrecher, Robert Abel, John D. Chodera, and Lingle Wang. Manuscript prior to publication: [bioRxiv] [input files and analysis scripts]

Biomolecular simulations under realistic macroscopic salt conditions. Gregory A. Ross, Ariën S. Rustenburg, Patrick B. Grinaway, Josh Fass, and John D. Chodera. Manuscript prior to publication: [bioRxiv] [simulation code] [results and analysis scripts]

L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH. Intlekofer A, Wang B, Liu H, Shah H, Carmona-Fontaine C, Rustenburg AS, Salah S, Gunner MR, Chodera JD, Cross JR, and Thompson CB. Nature Chemical Biology 13:494, 2017. [DOI] [PDF] [GitHub]

A water-mediated allosteric network governs activation of Aurora kinase A. Cyphers S, Ruff E, Behr JM, Chodera JD, and Levinson NM. Nature Chemical Biology 13:402, 2017. [DOI] [PDF] [GitHub]

Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin. Xu Jianing, Pham CG, Albanese SK, Dong Yiyu, Oyama T, Lee CH, Rodrik-Outmezguine V, Yao Z, Han S, Chen D, Parton DL, Chodera JD, Rosen N, Cheng EH, and Hsieh J. Journal of Clinical Investigation 126:3526, 2016. [DOI] [PDF]

Ensembler: Enabling high-throughput molecular simulations at the superfamily scale. Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle A. Beauchamp, and John D. Chodera. PLoS Computational Biology 12:e1004728, 2016. [DOI] [PDF] [bioRxiv] / data: [Dryad] / code: [GitHub]

Review articles

Markov state models of biomolecular conformational dynamicsJohn D. Chodera and Frank Noé. Curr. Opin. Struct. Biol., 25:135-144, 2014. [DOI] [PDF]

Entropy-enthalpy compensation: Role and ramifications for rational ligand designJohn D. Chodera and David L. Mobley. Annu. Rev. Biophys. 42:121, 2013. [DOI] [PDF]