Computational & Systems Biology Program

The John Chodera Lab

Research

Pictured: John Chodera
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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The John Chodera Lab

Publications

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]

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

Pictured: John Chodera

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

Members

Melissa  Boby
Melissa Boby

Graduate Student

Simon Boothroyd
Simon Boothroyd

Postdoctoral Fellow

Hannah Bruce
Hannah Bruce

Postdoctoral Fellow

Josh Fass
Josh Fass

Tri-I Computational Biology and Medicine Graduate Student

Erica Goldberger
Erica Goldberger

Research Technician

Erin Grundy
Erin Grundy

Lab Technician

Jiaye Guo
Jiaye Guo

Postdoctoral Fellow

Mehtap Isik
Mehtap Isik

Tri-I Chemical Biology Graduate Student

Binisha Karki
Binisha Karki

Research Technician

Ellen T. Mammen
Ellen T. Mammen

Administrative Assistant II

Andrea Rizzi

Tri-I Computational Biology and Medicine Graduate Student

Arien Rustenburg
Arien Rustenburg

Graduate Student

Ana Silveira
Ana Silveira

Postdoctoral Fellow

Chaya Stern
Chaya Stern

Graduate Student

Marcus Wieder
Marcus Wieder

Postdoctoral Fellow

Rafal Wiewiora

Tri-I Chemical Biology Graduate Student

Lab Alumni
Pictured: Steven Albanese
Steven K. Albanese

Graduate Student

Kyle A. Beauchamp, PhD
Kyle A. Beauchamp

Postdoctoral Research Fellow

Patrick Grinaway
Patrick Grinaway

Graduate Student

Sonya Hanson, DPhil
Sonya Hanson

Postdoctoral Research Fellow

Levi Naden

Postdoctoral Research Fellow

Daniel L. Parton, DPhil
Daniel L. Parton

Postdoctoral Research Fellow

Lucelenie Rodríguez-Laureano

Laboratory Technician

Gregory Ross

Postdoctoral Research Fellow

Lab Affilations

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)

Get in Touch

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:

  • Blueprint Medicines
    Provision of Services
  • Boehringer Ingelheim
    Provision of Services
  • Celgene
    Provision of Services
  • Foresite Labs LLC
    Provision of Services
  • OpenEye Scientific Software, Inc.
    Provision of Services

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, 2019 through disclosure submission in spring 2020). 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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