J. Fraser

发表

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

Kyle A. Barlow, Benjamin P. Roscoe, Benjamin A. Barad, 2015, bioRxiv.

Automated electron‐density sampling reveals widespread conformational polymorphism in proteins

H. Ng, J. Holton, J. Fraser, 2010, Protein science : a publication of the Protein Society.

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering

Frank von Delft, James S Fraser, Daniel A Keedy, 2018, eLife.

New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering

J. Wells, F. von Delft, J. Fraser, 2017, bioRxiv.

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.

Julie C. Mitchell, Andrej Sali, Dina Schneidman-Duhovny, 2016, Journal of molecular biology.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

Henry van den Bedem, James S. Fraser, Peter E. Wright, 2014, Proceedings of the National Academy of Sciences.

A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing

Benjamin J. Polacco, Robyn M. Kaake, Gwendolyn M. Jang, 2020, Nature.

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

Nicholas K. Sauter, Aaron S. Brewster, Jesse B. Hopkins, 2015 .

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

Jesse B. Hopkins, Andrew H. Van Benschoten, J. Holton, 2015, bioRxiv.

Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine.

Andrew H. Van Benschoten, M. Fischbach, Peter Cimermancic, 2014, Cell host & microbe.

Systematic Functional Prioritization of Protein Posttranslational Modifications

W. Lim, A. Burlingame, N. Krogan, 2012, Cell.

Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes

J. Fraser, J. Biel, G. Bhabha, 2014, Accounts of chemical research.

Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.

E. M. Thompson, J. Klinman, C. Gee, 2019, Journal of the American Chemical Society.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

Andrew H. Van Benschoten, M. Wall, P. Adams, 2014, Proceedings of the National Academy of Sciences.

Hidden alternate structures of proline isomerase essential for catalysis

D. Kern, J. Fraser, T. Alber, 2010 .

Automated identification of functional dynamic contact networks from X-ray crystallography

H. V. D. Bedem, P. Wright, J. Fraser, 2013 .

Integrative, dynamic structural biology at atomic resolution—it's about time

J. Fraser, H. van den Bedem, 2015, Nature Methods.

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

A. Ashworth, J. Irwin, B. Shoichet, 2020, Science Advances.

Protein structural ensembles are revealed by redefining X-ray electron density noise

J. Holton, J. Fraser, P. T. Lang, 2013, Proceedings of the National Academy of Sciences.

From systems to structure: bridging networks and mechanism.

Nevan J. Krogan, James S. Fraser, N. Krogan, 2013, Molecular cell.

E pluribus unum, no more: from one crystal, many conformations.

David A Sivak, David A. Sivak, James S Fraser, 2014, Current opinion in structural biology.

Accessing protein conformational ensembles using room-temperature X-ray crystallography

Nathaniel Echols, Tom Alber, Henry van den Bedem, 2011, Proceedings of the National Academy of Sciences.

CheShift-2 resolves a local inconsistency between two X-ray crystal structures

H. Scheraga, H. Dyson, J. Fraser, 2012, Journal of biomolecular NMR.

Objectively and automatically building multi-conformer ligand models in electron densities

H. V. D. Bedem, T. Day, K. Borrelli, 2017 .

Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2

N. Krogan, D. Agard, R. Stroud, 2020, Nature Chemical Biology.

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

Tanja Kortemme, Wendell A Lim, James S Fraser, 2012, Proceedings of the National Academy of Sciences.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

Saulo H. P. de Oliveira, M. Wall, S. Boutet, 2019, Proceedings of the National Academy of Sciences.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

Saulo H. P. de Oliveira, M. Wall, H. V. D. Bedem, 2019, Proceedings of the National Academy of Sciences.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.

Wilson, M. Wall, H. V. D. Bedem, 2019 .

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

Andrew H. Van Benschoten, M. Wall, P. Adams, 2015, bioRxiv.

Genetic interaction mapping informs integrative structure determination of protein complexes

John H. Morris, J. Bader, N. Krogan, 2020, Science.

Co-occurring alterations in the RAS-MAPK pathway limit response to MET inhibitor treatment in MET exon 14 skipping mutation positive lung cancer

E. Collisson, F. Kaye, I. Yeh, 2018 .

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

E. M. Thompson, S. Boutet, R. Sierra, 2020, IUCrJ.

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

E. M. Thompson, S. Boutet, R. Sierra, 2019, bioRxiv.

Bringing Diffuse X-ray Scattering Into Focus

M. Wall, J. Fraser, A. Wolff, 2017, bioRxiv.

Measuring and modeling diffuse scattering in protein X-ray crystallography

Andrew H. Van Benschoten, M. Wall, J. Fraser, 2015, bioRxiv.

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

D. Mobley, M. Wall, J. Fraser, 2019, Structural dynamics.

Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers

Benjamin A. Barad, T. Ideker, N. Krogan, 2018, bioRxiv.

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

J. Fraser, D. Keedy, H. van den Bedem, 2015, bioRxiv.

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

Miguel Correa Marrero, Robyn M. Kaake, Gwendolyn M. Jang, 2020, Science.

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.

H. V. D. Bedem, T. Day, K. Borrelli, 2018 .

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

D. Herschlag, J. Fraser, J. Biel, 2019, Proceedings of the National Academy of Sciences.

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

T. Day, K. Borrelli, A. Héliou, 2018, bioRxiv.

Synthetic group A streptogramin antibiotics that overcome Vat resistance

O. Chesneau, M. Jacobson, K. Borrelli, 2020, Nature.

Mining electron density for functionally relevant protein polysterism in crystal structures

J. Fraser, C. Jackson, 2010, Cellular and Molecular Life Sciences.

Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates

Benjamin A. Barad, R. Locksley, J. Fraser, 2020, Protein science : a publication of the Protein Society.

Dissecting the chitinolytic activity of mammalian chitinases

Benjamin A. Barad, R. Locksley, J. Fraser, 2019, bioRxiv.

Differences in the chitinolytic activity of mammalian chitinases on soluble and crystalline substrates

Benjamin A. Barad, R. Locksley, J. Fraser, 2019 .

Title: Co-occurring alterations in the RAS-MAPK pathway limit response to MET inhibitor treatment in MET exon 14 skipping mutation positive lung cancer

E. Collisson, F. Kaye, Wei Wu, 2019 .

EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

Benjamin A. Barad, P. Adams, Yifan Cheng, 2015, Nature Methods.

Resource Systematic Functional Prioritization of Protein Posttranslational Modifications

W. Lim, A. Burlingame, N. Krogan, 2012 .

Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2

Yurii S. Moroz, J. Irwin, B. Shoichet, 2022, bioRxiv.

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

J. Holton, A. Cohen, J. Fraser, 2022, Science advances.

Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit

J. Fraser, A. Frost, A. Myasnikov, 2020, Nucleic acids research.

Ligand binding remodels protein side-chain conformational heterogeneity

Saulo H. P. de Oliveira, J. Fraser, H. van den Bedem, 2022, eLife.

Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography

Benjamin A. Barad, R. Sierra, K. Tono, 2022, bioRxiv.

Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.

David A Sivak, Henry van den Bedem, David A. Sivak, 2014, Structure.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

Trey Ideker, Claudia Hernandez-Armenta, Brian K. Shoichet, 2020, bioRxiv.

Data publication with the structural biology data grid supports live analysis

Oleg V. Tsodikov, Stephen C. Blacklow, Amedeo Caflisch, 2016, Nature Communications.

Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases.

C. Craik, A. Renslo, J. Fraser, 2017, Journal of the American Chemical Society.

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

D. Herschlag, J. Fraser, J. Biel, 2022, Science advances.

Multiconformer synchrotron model of CypA at 260 K

H. V. D. Bedem, J. Holton, W. Weis, 2015 .

Multiconformer synchrotron model of CypA at 100 K

H. V. D. Bedem, J. Holton, W. Weis, 2015 .

Multiconformer fixed-target X-ray free electron (XFEL) model of CypA at 273 K

H. V. D. Bedem, J. Holton, W. Weis, 2015 .

High-resolution multiconformer synchrotron model of CypA at 273 K

H. V. D. Bedem, J. Holton, W. Weis, 2015 .

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2

Yurii S. Moroz, J. Irwin, B. Shoichet, 2022, bioRxiv.

Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel isotype-1 β-tubulin benzimidazole resistance mutation

J. Fraser, E. Andersen, E. Redman, 2022, bioRxiv.

Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.

Fabio Prati, Dan S. Tawfik, Dan S Tawfik, 2015, Journal of molecular biology.

From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

J. Benschop, F. Holstege, N. Krogan, 2013, Cell.

Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.

N. Krogan, W. Brown, Jeffrey R. Johnson, 2015, Cell reports.

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

D. Klepacki, A. Mankin, N. Vázquez-Laslop, 2022, Nature Structural & Molecular Biology.

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

A. Mankin, N. Vázquez-Laslop, J. Fraser, 2021, bioRxiv.

Ig-like domains on bacteriophages: a tale of promiscuity and deceit.

Zhou Yu, James S Fraser, Alan R Davidson, 2006, Journal of molecular biology.

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

Frank DiMaio, Yifan Song, James S. Fraser, 2016, bioRxiv.

Type 2 innate immunity regulates hair follicle homeostasis to control Demodex pathosymbionts

R. Locksley, M. Fassett, K. Bittinger, 2021, bioRxiv.

High-density grids for efficient data collection from multiple crystals

W. DeGrado, A. Kruse, W. Weis, 2016, Acta crystallographica. Section D, Structural biology.

EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

Nathaniel Echols, Frank DiMaio, Paul D Adams, 2015, Nature Methods.

The incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

Brian K. Shoichet, Ryan G. Coleman, James S. Fraser, 2014, Nature chemistry.

Co-occurring Alterations in the RAS–MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer

E. Collisson, F. Kaye, I. Yeh, 2019, Clinical Cancer Research.

Co-occurring genetic alterations in the RAS pathway promote resistance to MET inhibitor treatment in non-small cell lung cancer with a MET exon 14 skipping mutation

E. Collisson, F. Kaye, I. Yeh, 2018, bioRxiv.

Effects of α-tubulin acetylation on microtubule structure and stability

E. Nogales, M. Vendruscolo, J. Fraser, 2019, Proceedings of the National Academy of Sciences.

Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme

Alexander M. Wolff, James S. Fraser, Benjamin A. Barad, 2018, bioRxiv.

High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications

J. Fraser, A. Frost, A. Myasnikov, 2019, bioRxiv.

A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality.

Gabriel C Lander, James S Fraser, Mark A Herzik, 2019, Structure.

A multi-model approach to assessing local and global cryo-EM map quality

Gabriel C. Lander, James S. Fraser, Mark A. Herzik, 2017, bioRxiv.

Discovery of allosteric binding sites by crystallographic fragment screening.

F. von Delft, J. Fraser, T. Krojer, 2020, Current opinion in structural biology.

Computational design of a modular protein sense-response system

Michael C. Thompson, Tanja Kortemme, Mark Kelly, 2019, Science.

Immunoglobulin-like domains on bacteriophage: weapons of modest damage?

James S Fraser, Alan R Davidson, J. Fraser, 2007, Current opinion in microbiology.

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Gwendolyn M. Jang, N. Krogan, D. Agard, 2021, bioRxiv.

One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites

B. Shoichet, J. Fraser, M. Fischer, 2015, Chembiochem : a European journal of chemical biology.

Deep neural language modeling enables functional protein generation across families

Zachary Z. Sun, R. Socher, Ben Krause, 2021, bioRxiv.

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.

Dan S. Tawfik, J. Fraser, S. Floor, 2022, eLife.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Christopher J. Williams, Soon Wen Hoh, Colin M. Palmer, 2021, Nature Methods.

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

Genki Terashi, Daisuke Kihara, Grigore D. Pintilie, 2020, bioRxiv.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

Michael E. Wall, Mark Hunter, Nicholas K. Sauter, 2019, Proceedings of the National Academy of Sciences.

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

Benjamin A. Barad, O. Nureki, W. DeGrado, 2017, Proceedings of the National Academy of Sciences.

Promoting transparency and reproducibility in enhanced molecular simulations

Jakub Rydzewski, Toni Giorgino, Massimiliano Bonomi, 2019, Nature Methods.

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

A. Ashworth, J. Irwin, B. Shoichet, 2021, Science Advances.

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance

Kyle A. Barlow, Wesley M. Marin, Gabriel K. Reder, 2018, Biology Open.

Research Advance: Extending chemical perturbations of the Ubiquitin fitness landscape in a classroom setting

Kyle A. Barlow, Wesley M. Marin, J. Derisi, 2017, bioRxiv.

DNA-binding proteins meet their mismatch

J. Fraser, K. Kundert, 2020, Nature.

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Gwendolyn M. Jang, N. Krogan, D. Agard, 2021, Research square.

Rescue of conformational dynamics in enzyme catalysis by directed evolution

Dan S. Tawfik, Dan S Tawfik, James S Fraser, 2018, Nature Communications.

Flexible backbone sampling methods to model and design protein alternative conformations.

Tanja Kortemme, Noah Ollikainen, Colin A Smith, 2013, Methods in enzymology.

Synthetic group A streptogramin antibiotics that overcome Vat resistance

K. Borrelli, A. Brilot, J. Fraser, 2020, Nature.

Expanding the space of protein geometries by computational design of de novo fold families

Tanja Kortemme, Yang Zhang, Mark J. S. Kelly, 2020, Science.

Computational design of a modular protein sense-response system

Tanja Kortemme, Yao-Ming Huang, Daniel J. Mandell, 2019, Science.

Rescue of conformational dynamics in enzyme catalysis by directed evolution

Dan S. Tawfik, D. Kern, R. Otten, 2017, bioRxiv.

Automated identification of functional dynamic networks from X-ray crystallography

Henry van den Bedem, Gira Bhabha, James S. Fraser, 2013, Nature Methods.

Hydrogen–Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling

J. Klinman, Alexander D. Scouras, E. Poss, 2017, ACS central science.

Assessing positioning in enzymatic catalysis via ketosteroid isomerase conformational ensembles

D. Herschlag, J. Fraser, J. Biel, 2019, bioRxiv.

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

Henry van den Bedem, James S. Fraser, Daniel A. Keedy, 2015, bioRxiv.

Ensemble–function relationships to evaluate catalysis in the ketosteroid isomerase oxyanion hole

D. Herschlag, J. Fraser, J. Biel, 2021, bioRxiv.

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

Dan S. Tawfik, N. Elad, J. Fraser, 2021, bioRxiv.

Large language models generate functional protein sequences across diverse families

R. Socher, Ben Krause, Caiming Xiong, 2023, Nature Biotechnology.

Preprints for the life sciences

Philip E. Bourne, Carly Strasser, Harlan M. Krumholz, 2016, Science.

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

Yurii S. Moroz, J. Irwin, B. Shoichet, 2023, Proceedings of the National Academy of Sciences of the United States of America.

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature

A. Ashworth, J. Holton, A. Cohen, 2022, bioRxiv.

Molecular-dynamics simulation methods for macromolecular crystallography

D. Mobley, M. Wall, J. Fraser, 2022, bioRxiv.

Ligand binding remodels protein side chain conformational heterogeneity

Saulo H. P. de Oliveira, J. Fraser, H. van den Bedem, 2021, bioRxiv.

Bacteriophages inhibit and evade cGAS-like immune function in bacteria

J. Ren, J. Fraser, J. Bondy-Denomy, 2023, Cell.

qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps

Saulo H. P. de Oliveira, J. Fraser, D. Keedy, 2020, Protein science : a publication of the Protein Society.

qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps

Henry van den Bedem, Blake T. Riley, Gydo C. P. van Zundert, 2020, bioRxiv.

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

D. Mobley, M. Wall, J. Fraser, 2019, bioRxiv.

qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.

Henry van den Bedem, Pooja Suresh, Rasmus Fonseca, 2018, Journal of medicinal chemistry.

Model Selection for Biological Crystallography

Nathan S. Babcock, David A. Sivak, James S. Fraser, 2018, bioRxiv.

Bringing diffuse X-ray scattering into focus☆

Michael E Wall, James S Fraser, M. Wall, 2017, bioRxiv.

Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin

Christian N. Cunningham, J. Fraser, J. Corn, 2016, bioRxiv.

Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin

Michael C. Thompson, Jacob E. Corn, James S. Fraser, 2016, bioRxiv.

Measuring and modeling diffuse scattering in protein X-ray crystallography

Nicholas K Sauter, Lin Liu, Ana Gonzalez, 2015, Proceedings of the National Academy of Sciences.

Exposing hidden alternative backbone conformations 1 in X-ray crystallography using qFit 2 3

H. V. D. Bedem, J. Fraser, D. Keedy, 2015 .

Diffuse X-ray scattering to model protein motions.

Nicholas K Sauter, Paul D Adams, Michael E Wall, 2014, Structure.

Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization

M. Emerman, J. Fraser, L. Chelico, 2017, Nucleic acids research.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

Robyn M. Kaake, Gwendolyn M. Jang, Matthew J. O’Meara, 2020, Nature.

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

M. Klein, W. DeGrado, J. Fraser, 2015, Proceedings of the National Academy of Sciences.

A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo

J. Fraser, M. Ott, Morgan E. Diolaiti, 2023, bioRxiv.

Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico

J. Fraser, A. Broom, M. Thompson, 2020, Nature Communications.

Fragment-Based Hit Discovery via Unsupervised Learning of Fragment-Protein Complexes

Alpha A Lee, J. Fraser, N. London, 2022, bioRxiv.

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

R. Locksley, J. Fraser, M. Thompson, 2023, bioRxiv.

Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography

Benjamin A. Barad, R. Sierra, K. Tono, 2023, bioRxiv.

Conformational variation of proteins at room temperature is not dominated by radiation damage

Henry van den Bedem, James S. Fraser, Daniel A. Keedy, 2017, Journal of synchrotron radiation.

State of the structure address on MET receptor activation by HGF.

E. Collisson, J. Fraser, N. Jura, 2021, Biochemical Society transactions.

Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data

D. Herschlag, J. Fraser, F. Yabukarski, 2023, bioRxiv.

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

Alexandre Urzhumtsev, Paul D Adams, Pavel V Afonine, 2015, bioRxiv.

Accurate positioning of functional residues with robotics-inspired computational protein design

Jeffrey J. Gray, Roland A. Pache, J. Jeliazkov, 2022, Proceedings of the National Academy of Sciences of the United States of America.

An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS

D. Wemmer, J. Fraser, N. Echols, 2007, Molecular microbiology.

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

R. Locksley, J. Fraser, M. Thompson, 2023, bioRxiv.

Evolution of an enzyme conformational ensemble guides design of an efficient biocatalyst

J. Fraser, A. Broom, M. Thompson, 2020, bioRxiv.

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Dan S. Tawfik, J. Fraser, S. Floor, 2021, bioRxiv.

What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?

Massimiliano Bonomi, Kresten Lindorff-Larsen, James S. Fraser, 2020, J. Chem. Inf. Model..

Accurately positioning functional residues with robotics-inspired computational protein design

Jeffrey J. Gray, Roland A. Pache, J. Jeliazkov, 2021, bioRxiv.

Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain

E. Collisson, J. Fraser, N. Jura, 2023, bioRxiv.

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

J. Fraser, D. Keedy, H. van den Bedem, 2023, bioRxiv.

A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo.

J. Fraser, M. Ott, Morgan E. Diolaiti, 2023, PLoS pathogens.

Lineage-Specific Viral Hija cking of Non-canonical E 3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC 3 Activity Graphical

N. Krogan, W. Brown, Jeffrey R. Johnson, 2015 .

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Gwendolyn M. Jang, N. Krogan, D. Agard, 2021, bioRxiv.

interactomics of SARS-CoV-2

Gwendolyn M. Jang, R. Stroud, T. Kortemme, 2023 .

interactomics of SARS-CoV-2

Yang, Jen, N. Krogan, 2021 .

Chemoenzymatic Syntheses of Fluorine-18-Labeled Disaccharides from [18F] FDG Yield Potent Sensors of Living Bacteria In Vivo

M. Ohliger, David M. Wilson, J. Fraser, 2023, Journal of the American Chemical Society.

Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from [18F]FDG yield potent sensors of living bacteria in vivo

M. Ohliger, David M. Wilson, J. Fraser, 2023, bioRxiv.

Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis

M. Wall, H. V. D. Bedem, R. Sierra, 2019 .

Of problems and opportunities—How to treat and how to not treat crystallographic fragment screening data

G. Klebe, A. Heine, J. Fraser, 2022, bioRxiv.

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

D. Herschlag, J. Fraser, J. Biel, 2020, Proceedings of the National Academy of Sciences.

Measuring and modeling diffuse scattering in 3 protein X-ray crystallography

M. Wall, J. Fraser, N. Sauter, 2016 .

Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation

J. Fraser, E. Redman, J. Gilleard, 2023, PLoS pathogens.

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

D. Klepacki, A. Mankin, N. Vázquez-Laslop, 2022, Nature Structural & Molecular Biology.

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

Frank DiMaio, Yifan Song, Yifan Cheng, 2016, bioRxiv.