Projects per year
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Dive into the research topics where Darrin York is active. These topic labels come from the works of this person. Together they form a unique fingerprint.
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Collaborations and top research areas from the last five years
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Collaborative Research: Frameworks: Interoperable High-Performance Classical, Machine Learning and Quantum Free Energy Methods in AMBER
York, D. (PI)
7/15/22 → 6/30/27
Project: Research project
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Next-generation alchemical free energy methods and quantum/machine-learning models for drug discovery
York, D. (PI)
National Institute of General Medical Sciences
8/1/15 → 8/31/26
Project: Research project
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PRAC - Ensembles of molecular dynamics engines for assessing force fields, conformational change, and free energies of proteins and nucleic acids
Cheatham, T. E. (PI), York, D. (CoPI), Simmerling, C. (CoPI), Roitberg, A. E. (CoPI) & Case, D. (CoPI)
9/1/14 → 8/31/16
Project: Research project
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CDI-Type II: Mapping Complex Biomolecular Reactions with Large Scale Replica Exchange Simulations on National Production Cyberinfrastructure
Levy, R. (CoPI), York, D. (PI) & Jha, S. (CoPI)
10/1/11 → 9/30/16
Project: Research project
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Assessing Pavement Markings for Automated Vehicle Readiness
Cheatham, T. E. (PI), York, D. (CoPI), Simmerling, C. (CoPI), Roitberg, A. E. (CoPI), Walker, R. C. (CoPI) & Pike, A. A. (PI)
2/1/11 → 6/6/24
Project: Research project
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DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials
Zeng, J., Giese, T. J., Zhang, D., Wang, H. & York, D. M., Apr 14 2025, In: Journal of Chemical Information and Modeling. 65, 7, p. 3154-3160 7 p.Research output: Contribution to journal › Article › peer-review
Open Access15 Scopus citations -
DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials
Zeng, J., Zhang, D., Peng, A., Zhang, X., He, S., Wang, Y., Liu, X., Bi, H., Li, Y., Cai, C., Zhang, C., Du, Y., Zhu, J. X., Mo, P., Huang, Z., Zeng, Q., Shi, S., Qin, X., Yu, Z. & Luo, C. & 27 others, , May 13 2025, In: Journal of Chemical Theory and Computation. 21, 9, p. 4375-4385 11 p.Research output: Contribution to journal › Article › peer-review
Open Access22 Scopus citations -
FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks
Giese, T. J., Snyder, R., Piskulich, Z., Barletta, G. P., Zhang, S., McCarthy, E., Ekesan, Ş. & York, D. M., Jun 9 2025, In: Journal of Chemical Information and Modeling. 65, 11, p. 5273-5279 7 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction
Ojha, M., Hudson, L., Photenhauer, A., Zang, T., Lerew, L., Ekesan, Ş., Daniels, J., Nguyen, M., Paudyal, H., York, D. M., Ohi, M. D., Marchant, J., Bieniasz, P. D. & Koirala, D., Jul 8 2025, In: Nucleic acids research. 53, 12, gkaf583.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Recent Developments in Amber Biomolecular Simulations
Case, D., Cerutti, D. S., Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Ghazimirsaeed, M., Giambaşu, G. M., Giese, T. J., Götz, A. W., Harris, J. A., Kasavajhala, K., Lee, T. S., Li, Z., Lin, C., Liu, J., Miao, Y., Salomon-Ferrrer, R., Shen, J., Snyder, R. & Swails, J. & 11 others, , Aug 11 2025, In: Journal of Chemical Information and Modeling. 65, 15, p. 7835-7843 9 p.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations