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Author

James M. Holton

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Open access Sep 2026

Optimizing the connectivity of protein conformations to untangle ensemble refinement

The method successfully recovered the two original protein conformations from a previously published synthetic dataset that traps current refinement methods and produces models for deposited datasets of three separate 14–19 kDa proteins with greatly improved geometry and R-factors.

Spencer K. Passmore, James M. Holton, N. Zatsepin et al. · 0 citations
Open access Aug 2026

WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures

WaterFlow is introduced, a flow-matching-based generator model and confidence model for predicting the positions of ordered water molecules in protein structures that outperforms the existing state of the art at every precision level and quantifies the tradeoff between data quantity and data quality.

Vratin Srivastava, Huanghao Mai, Marcus D. Collins et al. · 0 citations

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