UCSF / Lawrence Berkeley National Laboratory
Info
Ernest L. Prien Professor and Chair, Department of Bioengineering and Therapeutic Sciences, UCSF. Faculty Scientist, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory. Associate Director, Quantitative Biosciences Institute (QBI). PhD with Tom Alber at UC Berkeley (protein dynamics and crystallography). Started independent career at UCSF in 2011. Full Professor since 2020; Department Chair since August 2023.
Pioneer in extracting conformational ensemble information from X-ray diffraction data. Lab spans structural biology, deep mutational scanning, and drug discovery. Strong commitment to open science (former ASAPbio board member). Co-host of “Tortured Proteins” podcast with Stephanie Wankowicz.
DiffUSE role
Jaime Fraser is a DiffUSE PI lead. His lab collects data at ALS Beamline 8.3.1 (directed by James Holton). The Fraser Lab is the origin of qFit (multi-conformer modeling software that forms the backend of Sampleworks) and has deep expertise in protein conformational dynamics — the core scientific question DiffUSE aims to address.
DiffUSE Team Members
| Name | Role | Affiliation |
|---|---|---|
| Jaime Fraser | PI Lead | UCSF / LBNL |
| Stephanie Wankowicz | Scientific Program Director, DiffUSE | Vanderbilt (formerly UCSF Fraser Lab) |
| James Holton | Beamline Scientist, ALS 8.3.1 | UCSF / LBNL |
| Justin Biel | Software Engineer | Radial (Fraser Lab alumnus) |
| Marcus Collins | Senior Machine Learning Scientist | Radial |
| Doris Mai | Scientist | Radial |
| Andy Burnim | Project Manager | Radial |
| Nozomi Ando | PI Lead (Data Collection at CHESS) | Cornell |
| Steve Meisburger | Staff Scientist | CHESS |
| Michael Wall | PI (MD Simulations) | Los Alamos National Laboratory |
| Karson Chrispens | Graduate Student (Sampleworks lead) | UCSF (Fraser Lab PhD student) |
| Kara Zielinski | Sample comparison analysis | DiffUSE team |
Source
Team roster from diffuse.science/members
Key UCSF Associates (in landscape context)
| Name | Relationship | Affiliation |
|---|---|---|
| Dr. Andrej Sali | RCSB PDB UCSF site head; IHM/integrative modeling | UCSF / RCSB PDB |
| Thomas Ferrin | ChimeraX PI; RBVI Director | UCSF |
| Thomas Goddard | ChimeraX lead developer | UCSF |
| Dr. Arthur Zalevsky | RCSB PDB / PDB-IHM developer | UCSF |
| Dr. Jared Sagendorf | RCSB PDB developer | UCSF |
Beamline Access
| Beamline | Facility | Use |
|---|---|---|
| Beamline 8.3.1 (TomAlberTron) | ALS, LBNL | Primary MX data collection (lysozyme, Mac1, etc.) |
| Collaborators also use SSRL | SLAC | Fragment screening / VatD work (published 2025) |
Key Relationships in Landscape
- Heads Participating Research Team at ALS Beamline 8.3.1 with James Holton
- Stephanie Wankowicz was Fraser Lab postdoc; now runs DiffUSE as Scientific Program Director
- Frequent co-author with Paul Adams (PHENIX), Aaron Brewster (DIALS), James Holton
- Michael Wall (Los Alamos) provides MD simulation diffuse data for DiffUSE
- Nozomi Ando (Cornell/CHESS) is the complementary DiffUSE PI for data collection
- Lab developed qFit, which underpins Sampleworks (Karson Chrispens)
- Dr. Andrej Sali and Fraser are both at UCSF and co-authored the 2015 wwPDB IHM Task Force paper
- Fraser also collaborates with Frank DiMaio (University of Washington) — relevant to modeling/prediction side
Selected Key Publications (DiffUSE-relevant)
- Bayesian multi-state modeling from X-ray data (with Hancock, Holton, Adams, Sali — bioRxiv 2025)
- Mac1 ADP-ribosylhydrolase as SARS-CoV-2 therapeutic target (bioRxiv 2025)
- Discovery of AVI-6451 Mac1 inhibitor (J Med Chem 2026)
- Conformational ensembles and binding entropy in Mac1 (with Wankowicz — bioRxiv 2025)
modeling #datacollection #dataprocessing #encoding #sampleprep