Computational & Systems Biology Program
The John Chodera Lab
The Chodera lab uses computation and experiments to develop quantitative, multiscale models of the effects of small molecules on biomolecular macromolecules and cellular pathways. To do this, the group utilizes physical models and rigorous statistical mechanics, with the overall goals of engineering novel therapeutics and tools for chemical biology, as well as understanding the physical driving forces behind ligand recognition the evolution of resistance mutations.
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 calculations. Kevin 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]
John Chodera, PhD
- Computational chemist John Chodera uses statistical mechanics, molecular modeling, and automated biophysical experiments to help identify new potential therapeutics and investigate mechanisms of drug resistance in cancer.
- PhD, University of California, San Francisco
- [email protected]
- Email Address
- Louis V. Gerstner Young Investigator Award (2013)
- QB3-Berkeley Distinguished Postdoctoral Fellowship, University of California, Berkeley (2008)
- IBM Predoctoral Fellowship (2005)
- Howard Hughes Medical Institute Predoctoral Fellowship (2000)
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Doctors and faculty members often work with pharmaceutical, device, biotechnology, and life sciences companies, and other organizations outside of MSK, to find safe and effective cancer treatments, to improve patient care, and to educate the health care community.
MSK requires doctors and faculty members to report (“disclose”) the relationships and financial interests they have with external entities. As a commitment to transparency with our community, we make that information available to the public.
John Chodera discloses the following relationships and financial interests:
OpenEye Scientific Software, Inc.
Provision of Services
Redesign Science Inc.
Ownership / Equity Interests; Provision of Services (uncompensated)
The information published here is for a specific annual disclosure period. There may be differences between information on this and other public sites as a result of different reporting periods and/or the various ways relationships and financial interests are categorized by organizations that publish such data.
This page and data include information for a specific MSK annual disclosure period (January 1, 2020 through disclosure submission in spring 2021). This data reflects interests that may or may not still exist. This data is updated annually.