mx cryo-em computational software-dev
CUNY Advanced Science Research Center
Info
Associate Professor (promoted September 2025) at the Structural Biology Initiative of the CUNY Advanced Science Research Center. Develops experimental and computational methods to control proteins by biasing toward specific conformations underlying allostery, ligand binding, and catalysis. Lead of qFit 3, the open-source (MIT license) automated multi-conformer modeling tool for X-ray crystallographic and single-particle cryo-EM density maps. qFit generates parsimonious multiconformer models that represent conformational heterogeneity more faithfully than single-conformer models.
DiffUSE relevance
qFit is the software tool most directly connected to DiffUSE’s scientific goals. It originated in the Jaime Fraser lab ecosystem (Fraser Lab / ExcitedStates GitHub), and Keedy was a key figure in the Fraser Lab during the formative years of multi-conformer modeling. Diffuse scattering provides the next layer of information beyond what qFit can extract from Bragg data alone.
Key Relationships
- qFit 3 — lead developer (ExcitedStates/qfit-3.0 on GitHub)
- Jaime Fraser — Fraser Lab community; qFit originated in the Fraser / Alber lineage at UCSF
- Marcus Fischer — parallel multi-conformer community (FLEXR at St. Jude)
- Stephanie Wankowicz — former Fraser Lab; DiffUSE Scientific Program Director; qFit co-author
- CUNY Structural Biology Initiative
Sources
- CUNY profile: https://www.gc.cuny.edu/people/daniel-keedy
- ASRC profile: https://asrc.gc.cuny.edu/people/daniel-keedy/
- qFit 3 paper (Riley et al., Protein Science 2021): https://pubmed.ncbi.nlm.nih.gov/33210433/
- qFit software: https://github.com/ExcitedStates/qfit-3.0