Computational & Systems Biology Program

The John Chodera Lab

John Chodera, PhD

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.

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Featured News

In the Lab

Two clusters of colored blobs with a diagram in the middle

Computational “Hive Mind” Helps Scientists Solve an Enzyme’s Cryptic Movements

The breakthrough gives an unprecedented look at the varied and shifting poses of a protein in action.

Publications Highlights

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]

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People

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

Members

Maria A. Castellanos
Postgraduate Research Fellow

Ariana Clerkin
Postgraduate Research Fellow

Ellen T. Mammen
Senior Administrative Assistant

Sukrit Singh
Postdoctoral Research Fellow

Devany West

Postgraduate Research Fellow

Lab Alumni

Pictured: Steven Albanese — Steven K. Albanese
Principal Scientist, Schrödinger, Inc in New York, NY

Kyle A. Beauchamp, PhD — Kyle A. Beauchamp
Postdoctoral Research Fellow

Ashleigh Donnellan
Administrative Assistant

Josh Fass
Tri-I Computational Biology and Medicine Graduate Student

Sonya Hanson, DPhil — Sonya Hanson
Postdoctoral Research Fellow

Christopher Iacovella
Software Scientist

Mehtap Isik
Tri-I Chemical Biology Graduate Student

Hugo MacDermott-Opeskin
Software Scientist

Daniel L. Parton, DPhil — Daniel L. Parton
Postdoctoral Research Fellow

Andrea Rizzi
Tri-I Computational Biology and Medicine Graduate Student

Lucelenie Rodríguez-Laureano

Laboratory Technician

Mia Rosenfeld

Visiting Investigator

Gregory Ross

Postdoctoral Research Fellow

Jenke Scheen
Postdoctoral Research Scholar

Ashley Souffront

Project Coordinator

Lily Wang

Consultant

Rafal Wiewiora
Tri-I Chemical Biology Graduate Student

Lab Affiliations

Achievements

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)

Open Positions

To learn more about available postdoctoral opportunities, please visit our Career Center

To learn more about compensation and benefits for postdoctoral researchers at MSK, please visit Resources for Postdocs

Get in Touch

[email protected]

Lab Head Email

Disclosures

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:

Interline Therapeutics LLC
Equity; Professional Services and Activities
OpenEye Scientific Software, Inc.
Professional Services and Activities

Ventus Therapeutics
Professional Services and Activities

The information published here is a complement to other publicly reported data and 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, 2023 through disclosure submission in spring 2024). This data reflects interests that may or may not still exist. This data is updated annually.

Learn more about MSK’s COI policies here. For questions regarding MSK’s COI-related policies and procedures, email MSK’s Compliance Office at [email protected].

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