Computational & Systems Biology Program

The John Chodera Lab

Research

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

john.chodera@choderalab.org: Email Address

Members

Viktor Belay

Graduate Student

Maria A. Castellanos

Postdoctoral Research Fellow

Ariana Clerkin

Postdoctoral Research Fellow

Aakash Davasam

Graduate Student

Ayush Deep

Graduate Student

Benjamin Kaminow

Graduate Student

Kendall Lemons

Graduate Student

Ellen T. Mammen

Senior Administrative Assistant

Melissa Pathil

Graduate Student

Alexander Payne

Postdoctoral Research Fellow

Mark Polk

Research Technician

Iván Pulido

Software Scientist

Sukrit Singh

Postdoctoral Research Fellow

Yuanqing Wang

Visiting Investigator

Jessica White

Graduate Student

Shuai Yan

Graduate Student

Steven K. Albanese

Principal Scientist, Schrödinger, Inc in New York, NY

Kyle A. Beauchamp

Postdoctoral Research Fellow

Julie Behr

Graduate Student

Simon Boothroyd

Postdoctoral Fellow

Hannah Bruce

Postdoctoral Fellow

Liza Casella

Research Technician

Ashleigh Donnellan

Administrative Assistant

David Dotson

Software Scientist

Josh Fass

Tri-I Computational Biology and Medicine Graduate Student

Erica Goldberger

Research Assistant

Patrick Grinaway

Graduate Student

Erin Grundy

Lab Technician

Jiaye Guo

Postdoctoral Fellow

Sonya Hanson

Postdoctoral Research Fellow

Michael Henry

Software Scientist

Christopher Iacovella

Software Scientist

Mehtap Isik

Tri-I Chemical Biology Graduate Student

Binisha Karki

Research Technician

Hugo MacDermott-Opeskin

Software Scientist

Levi Naden

Postdoctoral Research Fellow

Daniel L. Parton

Postdoctoral Research Fellow

Michael Retchin

Graduate Student

Andrea Rizzi

Tri-I Computational Biology and Medicine Graduate Student

Lucelenie Rodríguez-Laureano

Laboratory Technician

Mia Rosenfeld

Visiting Investigator

Gregory Ross

Postdoctoral Research Fellow

Dominic Rufa

Graduate Student

Arien Rustenburg

Graduate Student

Jenke Scheen

Postdoctoral Research Scholar

Ana Silveira

Postdoctoral Fellow

Ashley Souffront

Project Coordinator

Chaya Stern

Graduate Student

Kenichiro Takaba

Visiting Investigator

Andrea Volkamer

Collaborator

Lily Wang

Consultant

Devany West

Postgraduate Research Fellow

Marcus Wieder

Postdoctoral Fellow

Rafal Wiewiora

Tri-I Chemical Biology Graduate Student

Ivy Zhang

Graduate Student

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

john.chodera@choderalab.org

Lab Head Email

Disclosures

Members of the MSK Community 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. These activities outside of MSK further our mission, provide productive collaborations, and promote the practical application of scientific discoveries.

MSK requires doctors, faculty members, and leaders 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. Not all disclosed interests and relationships present conflicts of interest. MSK reviews all disclosed interests and relationships to assess whether a conflict of interest exists and whether formal COI management is needed.

John Chodera discloses the following relationships and financial interests:

Achira, Inc.
Equity; Fiduciary Role / Position
Interline Therapeutics LLC
Equity
OpenEye Scientific Software, Inc.
Professional Services and Activities

Pico Therapeutics, Inc.
Equity
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, 2024 through disclosure submission in spring 2025). 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 ecoi@mskcc.org.

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