Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields

This repository is associated with the LiveCoMS perpetual review article titled "Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields". The LiveCoMS publication is available here.

List of Authors

• Chapin E. Cavender, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
• David A. Case, Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ, USA
• Julian C.-H. Chen, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA and Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH, USA
• Lillian T. Chong, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
• Daniel A. Keedy, Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA and Department of Chemistry and Biochemistry, City College of New York, New York, NY, USA and PhD Programs in Biochemistry, Biology, and Chemistry, CUNY Graduate Center, New York, NY, USA
• Kresten Lindorff-Larsen, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
• David L. Mobley, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
• O. H. Samuli Ollila, Institute of Biotechnology, University of Helsinki, Helsinki, Finland and VTT Technical Research Centre of Finland, Espoo, Finland
• Chris Oostenbrink, Institute for Molecular Modeling and Simulation, BOKU University, Vienna, Austria
• Paul Robustelli, Department of Chemistry, Dartmouth College, Hanover, NH, USA
• Vincent A. Voelz, Department of Chemistry, Temple University, Philadelphia, PA, USA
• Michael E. Wall, Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA and The Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
• David C. Wych, Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA and The Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
• Michael K. Gilson, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA

How to cite

Please use the following citation to reference this work:

Cavender, C. E., Case, D. A., Chen, J. C.-H., Chong, L. T., Keedy, D. A., Lindorff-Larsen, K., Mobley, D. L., Ollila, O. H. S., Oostenbrink, C., Robustelli, P., Voelz, V. A., Wall, M. E., Wych, D. C., Gilson, M. K. (2025). Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0]. Living Journal of Computational Molecular Science, 6(1), 3871. https://doi.org/10.33011/livecoms.6.1.3871

BibTeX:

@article{cavender_structure-based_2025,
    title={Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields \[Article v1.0\]},
    volume={6},
    url={https://livecomsjournal.org/index.php/livecoms/article/view/v6i1e3871},
    doi={10.33011/livecoms.6.1.3871},
    number={1},
    journal={Living Journal of Computational Molecular Science},
    author={Cavender, Chapin E. and Case, David A. and Chen, Julian C.-H. and Chong, Lillian T. and Keedy, Daniel A. and Lindorff-Larsen, Kresten and Mobley, David L. and Ollila, O. H. Samuli and Oostenbrink, Chris and Robustelli, Paul and Voelz, Vincent A. and Wall, Michael E. and Wych, David C. and Gilson, Michael K.},
    year={2025},
    month={Oct.},
    pages={3871}
}

Paper writing as code development

This paper is being developed as a living document, open to changes from the community. You can read more about the concept of writing a paper in the same way one would write software code in the essay "Paper writing as code development". If you have comments or suggestions, we welcome them! Please submit them as issues to this GitHub repository so they can be recorded and given credit for the contribution. Specific changes can be proposed via pull requests.

List of Released Versions

• v0.1: Initial submission to LiveCoMS. Posted as a preprint on arXiv.
• v0.2: Revised submission to LiveCoMS after peer review.
• v1.0: Accepted and published in LiveCoMS at https:doi.org/10.33011/livecoms.6.1.3871.

Changelog

• 2025-09-17 v0.2 Revisions from LiveCoMS peer review.
• 2025-10-25 v1.0 Copy editing after acceptance in LiveCoMS.