Research
- Modeling
WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures
Opens on biorxiv.org/content/10.64898/2026.08.26.747373v1
A flow-matching generator and confidence model for predicting the positions of ordered water molecules in protein structures. WaterFlow outperforms the existing state of the art at every precision level, and its novel predictions often fall on positive difference density, placing waters at sites the original depositions omitted. Preprint, bioRxiv. DOI: 10.64898/2026.08.26.747373
- Scholarly Work
- Modeling
Recovering Conformational Heterogeneity from the Protein Data Bank at Scale
Opens on thestacks.org/publications/qfit-at-scale
An ensemble dataset of over 60,000 structures. Applying qFit to re-refined PDB entries better than 2 Å to recover latent conformational heterogeneity at scale — the largest dataset of experimentally derived ensemble models. DOI: 10.82153/pff0-ck46
- Scholarly Work
- Modeling
Supplying a user-defined bulk solvent map for refinement
Opens on thestacks.org/publications/method-bulksolvent
A patch to Phenix refinement that lets users supply their own bulk solvent map in place of the default flat binary mask, opening refinement to MD, 3D-RISM and neural-network solvent models. DOI: 10.82153/2me0-hd96
- Scholarly Work
- Modeling
sampleworks: A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation
Opens on thestacks.org/publications/sampleworks-release
A modular framework for generating and evaluating biomolecular conformational ensembles from structure predictors guided by experimental data, benchmarked across Boltz-2, Protenix and RosettaFold3. DOI: 10.82153/jkxj-tw08
- Scholarly Work