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John Damon Chodera

Formats
  1. Journal Article (74)
  2. Meeting Abstract (33)
  3. Review (7)
  4. Correspondence (1)
  5. Editorial (1)
  6. Guidelines (1)
  7. Research Letter (1)
Groups
  1. Center for Molecular Imaging and Biotechnology (CMIB) (118)
  2. Computational and Structural Biology Program Faculty (118)
  3. GSK Faculty (118)
  4. Sloan Kettering Institute Faculty (118)
  5. MSK Grad Students (65)
  6. Sloan Kettering Institute Postdocs (33)

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

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Years
  1. 2025 (3)
  2. 2024 (9)
  3. 2023 (10)
  4. 2022 (11)
  5. 2021 (12)
  6. 2020 (7)

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Publications
  1. Biophysical Journal (19)
  2. Journal of Chemical Theory and Computation (14)
  3. Journal of Computer-Aided Molecular Design (13)
  4. Abstracts of Papers of the American Chemical Society (11)
  5. Journal of Chemical Information and Modeling (7)
  6. Journal of Physical Chemistry B (7)

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Publishers
  1. American Chemical Society (42)
  2. Cell Press (22)
  3. Springer (15)
  4. Nature Publishing Group (11)
  5. Royal Society of Chemistry (4)
  6. eLife Sciences Publications Ltd. (4)

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Results (118)

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  • Development and benchmarking of the open force field initiative self-consistent force field for proteins and small molecules
    Meeting Abstract

    Cavender, C. E.; Behara, P. K.; Friedman, A. J.; Horton, J. T.; McIsaac, A. R.; Smith, L. G.; Thompson, M. W.; Wagner, J.; Wang, L.; Westbrook, B. R.; more...
    Biophysical Journal (2025)

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  • Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding
    Journal Article

    Singh, S.; Gapsys, V.; Aldeghi, M.; Schaller, D.; Rangwala, A. M.; White, J. B.; Bluck, J. P.; Scheen, J.; Glass, W. G.; Guo, J.; more...
    Journal of Physical Chemistry B (2025)

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  • The need for continuing blinded pose- and activity prediction benchmarks
    Review

    Kramer, C.; Chodera, J.; Damm-Ganamet, K. L.; Gilson, M. K.; Gùˆnther, J.; Lessel, U.; Lewis, R. A.; Mobley, D.; Nittinger, E.; Pecina, A.; more...
    Journal of Chemical Information and Modeling (2025)

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  • Benchmarking cross-docking strategies in kinase drug discovery
    Journal Article

    Schaller, D. A.; Christ, C. D.; Chodera, J. D.; Volkamer, A.
    Journal of Chemical Information and Modeling (2024)

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  • Nutmeg and SPICE: Models and data for biomolecular machine learning
    Journal Article

    Eastman, P.; Pritchard, B. P.; Chodera, J. D.; Markland, T. E.
    Journal of Chemical Theory and Computation (2024)

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  • Development and benchmarking of a self-consistent force field for proteins and small molecules from open force field
    Meeting Abstract

    Cavender, C. E.; Behara, P. K.; Dotson, D. L.; Friedman, A. J.; Gokey, T.; Horton, J. T.; Pulido, I.; Thompson, M. W.; Wagner, J.; Wang, L.; more...
    Biophysical Journal (2024)

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  • 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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  • Neural network potentials for enabling advanced small-molecule drug discovery and generative design
    Review

    Barnett, S.; Chodera, J. D.
    Gen Biotechnology (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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  • EspalomaCharge: Machine learning-enabled ultrafast partial charge assignment
    Guidelines

    Wang, Y.; Pulido, I.; Takaba, K.; Kaminow, B.; Scheen, J.; Wang, L.; Chodera, J. D.
    Journal of Physical Chemistry A (2024)

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