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MSK Grad Students

  1. "John Chodera"
Formats
  1. Journal Article (47)
  2. Meeting Abstract (17)
  3. Review (1)
Groups
  1. GSK Faculty (65)
  2. Sloan Kettering Institute Faculty (65)
  3. Computational Biology Program Faculty (60)
  4. Center for Molecular Imaging and Biotechnology (56)
  5. Sloan Kettering Institute Postdocs (26)
  6. Center for Hematologic Malignancies (14)

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People
  1. John Chodera (65)
  2. Arien Rustenburg (14)
  3. Steven Albanese (12)
  4. Mehtap Isik (10)
  5. Rafal Wiewiora (10)
  6. Andrea Rizzi (9)

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Years
  1. 2024 (3)
  2. 2023 (3)
  3. 2022 (3)
  4. 2021 (10)
  5. 2020 (6)
  6. 2019 (8)

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Publications
  1. Biophysical Journal (10)
  2. Journal of Computer-Aided Molecular Design (10)
  3. Journal of Chemical Theory and Computation (6)
  4. Abstracts of Papers of the American Chemical Society (5)
  5. Journal of Physical Chemistry B (4)
  6. Chemical Science (3)

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Publishers
  1. American Chemical Society (17)
  2. Cell Press (12)
  3. Springer (10)
  4. Nature Publishing Group (8)
  5. Royal Society of Chemistry (4)
  6. eLife Sciences Publications Ltd. (3)

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Results (65)


Citation style sort is year ascending, and then by author or title. Author ascending is default.
  • An efficient protocol for accurately triaging molecules in the development of a SARS-CoV-2 main protease inhibitor
    Meeting Abstract

    Payne, A. M.; Kaminow, B.; Chodera, J. D.
    Biophysical Journal (2024)

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  • Machine-learned molecular mechanics force fields from large-scale quantum chemical data
    Journal Article

    Takaba, K.; Friedman, A. J.; Cavender, C. E.; Behara, P. K.; Pulido, I.; Henry, M. M.; MacDermott-Opeskin, H.; Iacovella, C. R.; Nagle, A. M.; Payne, A. M.; more...
    Chemical Science (2024)

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  • OpenMM 8: Molecular dynamics simulation with machine learning potentials
    Journal Article

    Eastman, P.; Galvelis, R.; Peláez, R. P.; Abreu, C. R. A.; Farr, S. E.; Gallicchio, E.; Gorenko, A.; Henry, M. M.; Hu, F.; Huang, J.; more...
    Journal of Physical Chemistry B (2024)

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  • Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
    Journal Article

    Boby, M. L.; Fearon, D.; Ferla, M.; Filep, M.; Koekemoer, L.; Robinson, M. C.; The COVID Moonshot Consortium; Chodera, J. D.; Lee, A. A.; London, N.; more...
    Science (2023)

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  • Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex
    Journal Article

    Zhang, I.; Rufa, D. A.; Pulido, I.; Henry, M. M.; Rosen, L. E.; Hauser, K.; Singh, S.; Chodera, J. D.
    Journal of Chemical Theory and Computation (2023)

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  • Turning high-throughput structural biology into predictive inhibitor design
    Journal Article

    Saar, K. L.; McCorkindale, W.; Fearon, D.; Boby, M.; Barr, H.; Ben-Shmuel, A.; The COVID Moonshot Consortium; London, N.; von Delft, F.; Chodera, J. D.; more...
    Proceedings of the National Academy of Sciences of the United States of America (2023)

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  • End-to-end differentiable construction of molecular mechanics force fields
    Journal Article

    Wang, Y.; Fass, J.; Kaminow, B.; Herr, J. E.; Rufa, D.; Zhang, I.; Pulido, I.; Henry, M.; Bruce Macdonald, H. E.; Takaba, K.; more...
    Chemical Science (2022)

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  • SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction
    Journal Article

    Grosjean, H.; Işık, M.; Aimon, A.; Mobley, D.; Chodera, J.; von Delft, F.; Biggin, P. C.
    Journal of Computer-Aided Molecular Design (2022)

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  • GCN2 kinase activation by ATP-competitive kinase inhibitors
    Journal Article

    Tang, C. P.; Clark, O.; Ferrarone, J. R.; Campos, C.; Lalani, A. S.; Chodera, J. D.; Intlekofer, A. M.; Elemento, O.; Mellinghoff, I. K.
    Nature Chemical Biology (2022)

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  • Development and benchmarking of Open Force Field v1.0.0-the Parsley small-molecule force field
    Journal Article

    Qiu, Y.; Smith, D. G. A.; Boothroyd, S.; Jang, H.; Hahn, D. F.; Wagner, J.; Bannan, C. C.; Gokey, T.; Lim, V. T.; Stern, C. D.; more...
    Journal of Chemical Theory and Computation (2021)

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