Author

James Fraser

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 4 Biochemistry· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Assay:structural biology· 4 Approach:deep learning· 3 Research Focus:protein folding & dynamics· 3 Research Focus:protein structure prediction· 3 Assay:cryo-EM· 2 Approach:experimental assay· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

Alexandre Urzhumtsev· 2 shared Andrew H Van Benschoten· 2 shared Daniel A Keedy· 2 shared Henry van den Bedem· 2 shared Pavel Afonine· 2 shared Aaron S Brewster· 1 shared Aina E Cohen· 1 shared Ana Gonzalez· 1 shared

Activity by Year

2015-2016 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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2 shared papersBiophysics

Alexandre Urzhumtsev

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

Ray Yu-Ruei Wang, Yifan Song, Benjamin Barad, Yifan Cheng, James Fraser, Frank DiMaio

This paper introduces an automated method to refine atomic structures from near-atomic-resolution cryo-EM maps, improving model geometry and fit-to-density while detecting and correcting backbone placement errors.

bioRxiv · Apr 26, 2016Biochemistry

Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

Daniel A Keedy, James Fraser, Henry van den Bedem

This paper introduces qFit, a method to identify hidden alternative backbone conformations in X-ray crystallography, revealing peptide flips and glycine movements in HIV protease.

PLOS Computational Biology · Oct 27, 2015Peer-reviewedBiophysics

Mapping the Conformational Landscape of a Dynamic Enzyme by XFEL and Multitemperature Crystallography

Daniel A Keedy, Lillian R Kenner, Matthew Warkentin, Rahel Woldeyes, Michael C Thompson, Aaron S Brewster, Andrew H Van Benschoten, Elizabeth L Baxter, Jesse B Hopkins, Monarin Uervirojnangkoorn, Scott E McPhillps, Jinhu Song, Roberto Alonso-Mori, James M Holton, William I Weis, , James Fraser

This study uses XFEL and multitemperature crystallography to analyze the conformational changes in cyclophilin A, revealing temperature-dependent conformational heterogeneity and a conformation shuffling model.

eLife · Sep 30, 2015Peer-reviewedBiophysics

Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting

David Mavor, Participants in UCSF PUBS Class, James Fraser

The paper uses deep mutational scanning to analyze how chemical stresses affect ubiquitin's mutational tolerance in yeast, revealing stress-specific fitness defects.

bioRxiv · Aug 25, 2015Systems Biology

From deep TLS validation to ensembles of atomic models built from elemental motions

Alexandre Urzhumtsev, Pavel Afonine, Andrew H Van Benschoten, James Fraser, Paul D Adams

The paper introduces a framework to validate TLS matrices in X-ray refinement and generate structural ensembles consistent with these parameters.

bioRxiv · Jan 2, 2015Biophysics

Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

Andrew Van Benschoten, Pavel Afonine, Thomas Terwilliger, Michael Wall, Colin Jackson, Nicholas Sauter, Paul Adams, Alexandre Urzhumtsev, James Fraser

The paper introduces phenix.diffuse, a tool that calculates X-ray diffuse scattering from structural ensembles, demonstrating its application to TLS refinement in glycerophosphodiesterase GpdQ.

bioRxiv · Jan 2, 2015Biophysics