The Chodera lab combines expertise in theory, computation, and automated biophysical experiments to transform physics-based simulations into predictive models of drug binding, dynamics, and selectivity.


Photo Credit:  Peter Hellberg

John D. Chodera, PhD

email: john.chodera@choderalab.org / tel: 646.737.3319 / twitter: @jchodera / ORCID 0000-0003-0542-119X
Associate Member, Computational Biology Program, Sloan Kettering Institute
Associate Member, Memorial Sloan Kettering Cancer Center
Associate Professor, Physiology, Biophysics, and Systems Biology Program,
Weill Cornell Graduate School of Medical Sciences
BIH Einstein Visiting Professor, Charité Universitätmedizin, Berlin
CV | NIH Biosketchgoogle scholar citations ]
 


Current group members


LAB MANAGER

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Erin Grundy

LAB MANAGER / RESEARCH TECHNICIAN

email: erin.grundy@choderalab.org / tel: 646.888.3594 / ORCID 0000-0001-7094-1461
[ LinkedIn ]


POSTDOCS


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Hannah Bruce Macdonald

Postdoctoral research fellow

Theory and algorithms for scalable, adaptive free energy calculations
email: hannah.brucemacdonald@choderalab.org / ORCID 0000-0002-5562-6866
[ Google Scholar ]


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Jiaye Guo

Postdoctoral research fellow

Selective kinase inhibitor recognition and the emergence of drug resistance
email: jiaye.guo@choderalab.org / ORCID 0000-0001-7439-1479
[ Google Scholar ]


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Simon Boothroyd

XTALPI / OPEN FORCE FIELD CONSORTIUM Postdoctoral research fellow

Molecular mechanics force field parameterization using physical property datasets
email: simon.boothroyd@choderalab.org / ORCID 0000-0002-3456-1872
[ Google Scholar | ResearchGate ]


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Ana Silveira, Ph.D.

POSTDOCTORAL RESEARCH FELLOW

Theory and algorithms for free energy calculations and integrative Markov state models
email: ana.silveira@choderalab.org / ORCID 0000-0002-9419-3397
[ Google Scholar ]


Marcus Wieder, Ph.D.

FWF ERWIN SCHRÖDINGER POSTDOCTORAL RESEARCH FELLOW

Tautomer effects on ligand binding
email: marcus.wieder@choderalab.org / ORCID 0000-0003-2631-8415


GRADUATE STUDENTS


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Patrick Grinaway

Weill Cornell PHYSIOLOGY, BIOPHYSICS, AND Systems BIOLOGY GRADUATE STUDENT
Entry year: 2012

Advanced statistical sampling methods for free energy calculations; distributed computing
email: patrick.grinaway@choderalab.org / tel: 646.888.3729 / ORCID 0000-0002-9762-4201


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Chaya Stern

Tri-I Chemical Biology graduate student
Entry year: 2013 // NSF GRADUATE RESEARCH FELLOW

Bayesian forcefield parameterization and error propagation; large-scale and single molecule fluorescence data analysis.  
email: chaya.stern@choderalab.org / tel: 646.888.3052 / ORCID 0000-0001-6200-3993


Bas Rusternburg 3

Ariën Sebastiaan (Bas) Rustenburg

Weill CornelL Physiology, Biophysics, and Systems Biology graduate student
Entry year: 2013

Protonation state effects in biomolecular interactions; constant-pH methodologies; advanced techniques for isothermal titration calorimetry
email: bas.rustenburg@choderalab.org / tel: 646.888.3473 / ORCID: 0000-0002-3422-0613

LinkedIn |  Google Scholar Citations ]


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Mehtap Isik

Tri-I CHEMICAL BIOLOGY GRADUATE STUDENT // Doris J. Hutchison Fellow (2017-2018)
Entry year: 2014

Model systems for quantitative prediction of protein:ligand interactions with alchemical free energy methods
email: mehtap.isik@choderalab.org / tel: 646.888.3729 / ORCID: 0000-0002-6789-952X


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Rafal Wiewiora

Tri-I CHEMICAL BIOLOGY GRADUATE STUDENT // DoD Horizon cancer award recipient
Entry year: 2014

Conformational dynamics and chemical probe design of histone lysine methyltransferases (HKMTs);
Massively parallel molecular dynamics simulations on Folding@home; Markov State Modeling

email: rafal.wiewiora@choderalab.org / tel: 646.888.3729 / ORCID: 0000-0002-8961-7183

[google scholar citations | linkedin]


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Steven K. Albanese

Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences
Entry year: 2014

Free energy calculations and automated biophysical measurements to predict selectivity of small molecule kinase inhibitors and the functional impact of clinical kinase mutations; Massively parallel molecular dynamics simulations on Folding@home; kinase conformational dynamics; computer aided drug design; expression and purification of human kinases
email: steven.albanese@choderalab.org / tel: 646.888.3527 / ORCID: 0000-0003-0973-5030
[google scholar citations | CV |website | twitter]


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Andrea Rizzi

Tri-I COMPUTATIONAL BIOLOGY AND MEDICINE GRADUATE STUDENT
Entry year: 2014

Advanced methodologies and software design for scalable alchemical free energy calculations
email: andrea.rizzi@choderalab.org / tel: 646.888.3475 / ORCID: 0000-0001-7693-2013


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Josh Fass

Tri-I COMPUTATIONAL BIOLOGY AND MEDICINE GRADUATE STUDENT
Entry year: 2014

Langevin integrators and sampling; Markov state model theory; machine learning
email: josh.fass@choderalab.org / tel: 646.888.3729 / ORCID 0000-0003-3719-266X


ADMINISTRATIVE ASSISTANT

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Ashleigh Fowlkes

email: fowlkesa@mskcc.org  


FORMER MEMBERS


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Levi Naden, Ph.D.

POSTDOCTORAL RESEARCH FELLOW // MERCK kgga postdoctoral research fellow

Alchemical binding free energies; automated free energy workflow; large-scale chemical space exploration; efficient reweighting techniques; GPU computing
email: levi.naden@choderalab.org / tel: 646.888.3594 / ORCID 0000-0002-3692-5027


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Jessica Tom, Azim Dharani, Hersh Gupta, and Brennan Lee

2018 Summer UNDERGRADUATE Students


Lucelenie Rodríguez-Laureano

FORMER LABORATORY TECHNICIAN / LAB MANAGER

Current position: Medical Student, NYU School of Medicine

[ ORCIDLinkedIn ]


Gregory A. Ross, DPhil

FORMER POSTDOCTORAL RESEARCH FELLOW

Current position: Free Energy Senior Scientist, Schrödinger

websitegoogle scholar citations | ORCID ]


 

Sonya Hanson, DPhil

FORMER POSTDOCTORAL RESEARCH FELLOW

Current position: Joachim Frank lab, Columbia University

CV | website | science blog | twitter | google scholar citations | ORCID ]


Julie Behr 3

Julie M. Behr

Tri-I Computational Biology and Medicine graduate student


photo Credit:  Mitya Ku

Daniel L. Parton, DPhil

FORMER Postdoctoral research fellow

Current position: Lead Data Scientist, Bardess Group

[ google scholar citations | LinkedIn ]


Kyle A. Beauchamp, PhD

FORMER Postdoctoral research fellow

Current position: Computational Research Scientist, Counsyl

google scholar citations | LinkedIn ]


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Jan-Hendrik Prinz, PhD

FORMER Postdoctoral research fellow

Current position: Digital Solution Architect, Keylight GmbH

google scholar citations | LinkedIn ]


Sarah E. Boyce, PhD

FORMER Postdoctoral research fellow

Current position: Senior Scientist, Drug Discovery Applications GroupSchrödinger.

[ LinkedIn ]


Antonia S. J. S. Mey, PhD

Former summer visiting graduate student

Current position: Postdoctoral Research Associate, Julien Michel Group, University of Edinburgh

website | google scholarLinkedIn ]


Rosa Luirink, MSc

FORMER SUMMER VISITING GRADUATE STUDENT


Currently PhD candidate at Vrije Universiteit Amsterdam


Guillermo Pérez Hernández, PhD

FORMER SUMMER VISITING postdoctoral research fellow

Current position: Staff Scientist, Frank Noé group, Freie Universität Berlin

[ ResearchGate ]