Current Members
Alexander Matthew Payne
Position: Postoctoral Research Scholar
Email: alex.payne@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Tri-Institutional PhD Program in Chemical Biology (TPCB)
Projects
- Alchemical free energy calculations that can learn
- Machine learning for drug discovery
- Large-scale molecular dynamics simulations of transmembrane proteins
Benjamin Kaminow
Position: Graduate Student
Email: benjamin.kaminow@choderalab.org
Affiliations
- Tri-Institutional PhD Program in Computational Biology and Medicine (CBM)
Projects
- End-to-end differentiable fitting of molecular mechanics force fields
- Structure-based machine learning for enantiomer ranking prediction
Christopher Iacovella
Position: Software Scientist
Email: chris.iacovella@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Open Force Field Initiative (OpenFF)
Projects
- Machine learning potentials for drug discovery
- Optimization of molecular mechanics force fields
- Development of datasets for training and benchmarking machine learning potentials
David Dotson
Position: Software Scientist Consultant
Email: david.dotson@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Open Force Field Initiative, Open Molecular Software Foundation
- Datryllic LLC
Projects
- Folding@Home - OpenMM core continuous deployment automation
- Covid Moonshot - binding free energy automation for drug discovery
Ellen Mammen
Position: Senior Administrative Assistant
Email: mammene@mskcc.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Iván Pulido
Position: Software scientist - Bioinformatics software engineer
Email: ivan.pulido@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Projects
- Physics-based alchemical free energy calculations
- End-to-end differentiable fitting of molecular mechanics force fields
- Alchemical free energy calculations that can learn
- Machine learning for drug discovery
Jessica White
Position: Graduate Student
Email: jessica.white@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Tri-Institutional PhD Program in Computational Biology and Medicine (CBM)
Projects
- Assessment of mutant activity across the kinome
- Machine learning for drug discovery
John D Chodera
Position: Principal Investigator
Kendall Lemons
Position: Graduate Student
Email: kendall.lemons@choderalab.org
Affiliations
- Tri-Institutional PhD Program in Chemical Biology (TPCB)
Projects
Mike Henry
Position: Software Scientist
Email: mike.henry@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Open Free Energy https://openfree.energy/
Projects
- End-to-end differentiable fitting of molecular mechanics force fields
- Alchemical free energy calculations that can learn
- Machine learning for drug discovery
Sukrit Singh
Position: Damon Runyon Quantitative Biology Fellow / Postdoctoral Research Fellow
Email: sukrit.singh@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Joint Mentorship with Prof. Markus Seeliger (https://you.stonybrook.edu/mseeligerlab/)
- Folding@home Consortium (https://foldingathome.org)
Projects
- Mechanisms of resistance to kinase therapeutics
- Exascale molecular dynamics and enhanced sampling
- Markov state modeling of protein conformational ensembles
Viktor Belay
Position: Graduate Student
Email: viktor.belay@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Weill Cornell Physiology, Biophysics, and Systems Biology PhD Program (PBSB)
- Joint Mentorship with Richard Hite (https://www.mskcc.org/research/ski/labs/richard-hite)
Projects
- Small molecule discovery and research into allosteric activation for TMEM175
- Understanding the role of nucleotide binding in activation of IP3R
- Determining the structure and function of CLC6
Position:
Email: firstname.lastname@choderalab.org
Affiliations
- Weill Cornell Biochemistry and Structural Biology PhD Program
- Tri-Institutional PhD Program in Computational Biology and Medicine
- Tri-Institutional PhD Program in Chemical Biology
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences
- Berlin Institute of Health (BIH) Einstein Foundation - Stiftung Charité Group
- Joint Mentorship with Name (URL to lab homepage)
Projects
- End-to-end differentiable fitting of molecular mechanics force fields
- Alchemical free energy calculations that can learn
- Machine learning for drug discovery
- Large-scale molecular dynamics simulations of transmembrane proteins
Alumni
Alumni
Alex Li
Position: CBSP Summer Undergraduate Intern
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Computational Biology Summer Program (CBSP)
- Massachusetts Institute of Technology (MIT)
Ana Silveira
Position: Postoctoral Research Scholar
Email: ana.silveira@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Projects
- Theory and algorithms for free energy calculations and integrative Markov state models
Andrea Rizzi
Position: Graduate Student
Email: andrea.rizzi@choderalab.org
Affiliations
- Tri-Institutional PhD Program in Computational Biology and Medicine
Projects
- Advanced methodologies and software design for scalable alchemical free energy calculations
Arielle Tycko
Position: CBSP Summer Undergraduate Intern
Email: arielle.tycko@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Computational Biology Summer Program (CBSP) for Undergraduates
- Caltech, Computation and Neural Systems
Projects
- Structure-informed machine learning for the COVID Moonshot
Azim Dharani
Position: CBSP Summer Undergraduate Intern
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Computational Biology Summer Program (CBSP)
- Duke University
Ariën Sebastiaan (Bas) Rustenberg
Position: Graduate Student
Email: bas.rustenburg@choderalab.org
Affiliations
- Weill Cornell Physiology, Biophysics, and Systems Biology PhD Program
Projects
- Protonation state effects in biomolecular interactions
- constant-pH methodologies
- advanced techniques for isothermal titration calorimetry
Binisha Karki
Position: Research Technician
Email: binisha.karki@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Brennan Lee
Position: CBSP Summer Undergraduate Intern
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Computational Biology Summer Program (CBSP)
- Massachusetts Institute of Technology (MIT)
Projects
- Time-lagged Independent Components Analysis (TICA) Variant
- Developed a novel dimensionality reduction technique to industry standards for the analysis of protein dynamics simulations
Chaya Stern
Position: Graduate Student
Email: chaya.stern@choderalab.org
Affiliations
- Tri-Institutional PhD Program in Chemical Biology
Projects
- Bayesian forcefield parameterization and error propagation
- large-scale and single molecule fluorescence data analysis
Corey Taylor
Position: Postdoctoral Research Fellow
Email: corey.taylor.de@choderalab.org
Affiliations
- Berlin Institute of Health (BIH) Einstein Foundation - Stiftung Charité Group
- Charité Universitätsmedizin Berlin
- Joint Mentorship with Prof. Dr. Andrea Volkamer (https://volkamerlab.org/)
Projects
- Structure-informed machine learning with free energy calculations to predict and design kinase polypharmacology
Daniel L. Parton
Position: Postoctoral Research Fellow
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Darnell Granberry
Position: CBSP Summer Undergraduate Intern
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Computational Biology Summer Program (CBSP)
- Massachusetts Institute of Technology (MIT)
Projects
- Implemented the beginning of a "sandbox" environment for evaluating active-learning algorithms in drug discovery applications
David Bushiri
Position: Research Intern
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- TU Dortmund University
Projects
- Prediction of pKa-values of small molecules by applying machine learning methods
David Schaller
Position: Postdoctoral Research Fellow
Email: schaller.david89@gmail.com
Affiliations
- Charité Universitätsmedizin Berlin
- Bayer AG
- Joint Mentorship with Prof. Dr. Andrea Volkamer (https://volkamerlab.org/)
Projects
- Free Energy Calculations and Machine Learning for Kinase Drug Discovery with Focus on Mutations
Dominic Rufa
Position: Graduate Student
Email: dominic.rufa@choderalab.org
Affiliations
- Tri-Institutional PhD Program in Chemical Biology (TPCB)
Projects
- Nonequilibrium free energy calculations for drug discovery
Erica Goldberger
Position: Research Assistant; Lab Manager
Email: erica.goldberger@choderalab.org
Affiliations
- Memorial Sloan-Kettering Cancer Center (MSKCC)
Projects
- Exploiting turn-on fluorescence of FDA-approved kinase inhibitors in a universal probe of kinase inhibitor afinity
- Cell-free protein synthesis
- Protein-protein binding using ITC
Erin Grundy
Position: Lab Manager/Research Technician
Email: erin.grundy@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Projects
- Exploiting turn-on fluorescence of FDA-approved kinase inhibitors in a universal probe of kinase inhibitor afinity
- Cell-free protein synthesis
- Protein-protein binding using ITC
- Synthesis of kinase inhibitors encapsulated in nanoparticles
Guillermo Pérez Hernández
Position: Summer Visiting Postoctoral Research Fellow
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- German Academic Exchange Service, DAAD
Hannah Bruce Macdonald
Position: Postoctoral Research Fellow
Email: hannahbrucemacdonald@gmail.com
Affiliations
- Memorial Sloan-Kettering Cancer Center (MSKCC)
Projects
- Theory and algorithms for scalable, adaptive free energy calculations
Hersh Gupta
Position: CBSP Summer Undergraduate Intern
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Computational Biology Summer Program (CBSP)
- Brown University
Projects
- Built computational tools to study binding kinetics
Hugo MacDermott-Opeskin
Position: Software Scientist
Email: hugo.macdermott@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- AI-driven Structure-enabled Antiviral Platform (ASAP)
- Open Molecular Software Foundation (OMSF)
Ivy Zhang
Position: Graduate Student
Email: ivy.zhang@choderalab.org
Affiliations
- Tri-Institutional PhD Program in Computational Biology and Medicine (CBM)
Projects
- Alchemical free energy calculations for predicting the impact of point mutations on small molecule and protein binding
Jaime Rodríguez-Guerra Pedregal
Position: Postoctoral Research Fellow
Email: jaime.rogue@gmail.com
Affiliations
- Berlin Institute of Health (BIH) Einstein Foundation
- Stiftung Charité Group
- Joint Mentorship with Prof. Dr. Andrea Volkamer
Projects
- Scalable alchemical free energy calculations and machine learning for kinase drug discovery
Jan-Hendrik Prinz
Position: Postoctoral Research Fellow
Email: jan.prinz@gmx.de
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Projects
- High-performance computing, GPU Cluster
- Molecular modelling, Data clustering, Machine Learning
- {"Wet-lab experience"=>"Laboratory Automation / Liquid Handling Robots (Tecan, HP, Thermo Fisher, Mettler Toledo)"}
Jenke Scheen
Position: Postdoctoral Research Scholar
Email: jenke.scheen@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Open Molecular Software Foundation (OMSF)
- AI-driven Structure-enabled Antiviral Platform (ASAP)
Projects
- Free Energy calculations on Folding@Home
- Structure-informed AI methodologies for early-stage drug discovery
- Automated docking pipelines for open-source drug discovery
- Project support for ASAP discovery lead optimisation
- Science liaison for ASAP computational comp-chem core
Jessica Tom
Position: CBSP Summer Undergraduate Intern
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Computational Biology Summer Program (CBSP)
- Stonybrook University
Projects
- Characterization of clinically relevant c-Abl kinase mutants to determine drug susceptibility
Jiaye Guo
Position: Postoctoral Research Scholar
Email: jiaye.guo@choderalab.org
Affiliations
- Memorial Sloan-Kettering Cancer Center (MSKCC)
Projects
- kinase conformation sampling and drug discovery using enhanced sampling and machine learning
Josh Fass
Position: Graduate Student
Email: joshua.fass@gmail.com
Affiliations
- Tri-Institutional PhD Program in Computational Biology and Medicine (CBM)
Projects
- Langevin integrators and sampling; Markov state model theory; machine learning
Julie M. Behr
Position: Graduate Student
Affiliations
- Tri-Institutional PhD Program in Computational Biology and Medicine (CBM)
Kenichiro Takaba
Position: Visiting Investigator
Email: ken.takaba@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Pharmaceutical Research Center, Asahi Kasei Pharma Corporation
Projects
- Integration of structure-informed machine learning and biomolecular simulations to accelerate drug discovery
Karmen Čondić-Jurkić
Position: Postoctoral Research Fellow
Email: karmen.condic-jurkic@openforcefield.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Open Force Field Consortium
Projects
- Open Force Field Scientific Coordination
- Open Science Initiatives
Kyle A. Beauchamp
Position: Postoctoral Research Fellow
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Projects
- Markov state modeling theory and implementation;
- quantitative NMR measurements for conformational distributions
- Folding@Home distributed computing
Levi Naden
Position: Postoctoral Research Fellow
Email: levi.naden@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Merck KGGA Postoctoral Research Fellow
Projects
- Alchemical binding free energies;
- automated free energy workflow;
- large-scale chemical space exploration; efficient reweighting techniques;
- GPU computing
Liza Casella
Position: Research Technician
Email: casella.liza@gmail.com
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Projects
- Exploiting turn-on fluorescence of FDA-approved kinase inhibitors in a universal probe of kinase inhibitor afinity
Lucelenie Rodríguez-Laureano
Position: Lab Manager/Research Technician
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Marcus Wieder
Position: Postoctoral Research Scholar
Affiliations
- FWF Erwin Schrödinger Postoctoral Research Scholar
Mehtap Işık
Position: Graduate Student
Email: mehtap.isik.000@gmail.com
Affiliations
- Tri-Institutional PhD Program in Chemical Biology (TPCB)
Projects
- Model systems for quantitative prediction of protein:ligand interactions with alchemical free energy methods
Melissa Boby
Position: Graduate Student
Email: melissa.boby@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Weill Cornell Pharmacology PhD Program
- Joint Mentorship with Dr. Derek Tan (https://www.mskcc.org/research/ski/labs/derek-tan)
Projects
- COVID Moonshot
- Benchmarking alchemical free energy calculations
- Gigadocking with iteritive resampling for structure based drug discovery
Michael Retchin
Position:
Email: Michael.Retchin@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Tri-Institutional PhD Program in Computational Biology and Medicine (CBM)
Projects
- End-to-end differentiable fitting of molecular mechanics force fields
- Alchemical free energy calculations that can learn
- Machine learning for drug discovery
- Large-scale molecular dynamics simulations of transmembrane proteins
Patrick Grinaway
Position: Graduate Student
Email: patrick.grinaway@choderalab.org
Affiliations
- Weill Cornell Physiology, Biophysics, and Systems Biology PhD Program (PBSB)
Projects
- Advanced statistical sampling methods for free energy calculations; distributed computing
Rafal Wiewiora
Position: Graduate Student & Postdoctoral Research Scholar
Email: rafal.wiewiora@choderalab.org
Affiliations
- Tri-Institutional PhD Program in Chemical Biology (TPCB)
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Redesign Science
Projects
- Markov state modeling for drug discovery, in collaboration with Redesign Science
- Massively parallel molecular dynamics simulations on Folding@home
Robert Arbon
Position: Software Scientist Consultant
Email: robert.arbon@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Jean Golding Institute
- Redesign Science
Projects
- Adaptive Markov state model sampling
- Folding@home
- COVID Moonshot
- Automated free energy calculations for drug discovery
Rosa Luirink
Position: Summer Visiting Graduate Student
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Vrije Universiteit Amsterdam
Simon Boothroyd
Position: Postoctoral Research Fellow
Email: simon.boothroyd@choderalab.org
Affiliations
- XTALPI / Open Force Field Consortium
Projects
- Molecular mechanics force field parameterization using physical property datasets
Steven K. Albanese
Position: Graduate Student
Email: steven.albanese@choderalab.org
Affiliations
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences
Projects
- 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
Talia B. Kimber
Position: Graduate Student
Email: talia.kimber@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Charité Universitätsmedizin Berlin
- Freie Universitätsmedizin Berlin, Department of Mathematics and Computer Science
- Joint Mentorship with Prof. Dr. Andrea Volkamer (https://volkamerlab.org/)
- Joint Mentorship with Prof. Dr. Frank Noé (https://www.mi.fu-berlin.de/en/math/groups/ai4s/staff/noe/index.html)
Projects
- Machine learning for kinase drug discovery
Vivian Ye
Position: Summer Research High School Student Intern
Email: vivian.ye@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
Projects
- COVID Moonshot
William Glass
Position: Postoctoral Research Fellow
Email: william.glass@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Bayer AG
Projects
- Alchemical free energy calculations to asses the impact of point mutations for kinase drug discovery and small molecule binding
- Scalable alchemical free energy calculations for predicting drug resistance and susceptibility
- COVID Moonshot COVID-19 therapeutic development
Yuanqing Wang
Position: Graduate Sudent
Email: yuanqing.wang@choderalab.org
Affiliations
- Memorial Sloan Kettering Cancer Center (MSKCC)
- Weill Cornell Physiology, Biophysics, and Systems Biology PhD Program (PBSB)
Projects
- End-to-end differentiable fitting of molecular mechanics force fields
- Alchemical free energy calculations that can learn
- Machine learning for drug discovery
- Large-scale molecular dynamics simulations of transmembrane proteins