List of works - James S Fraser

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

scientific article published on 15 November 2018

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

scientific article published on 30 April 2020

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

journal article from 'bioRxiv' published in 2020

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

scientific article published on 20 December 2021

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

scholarly article published 19 April 2017

A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin

scientific article published on 07 September 2023

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

scientific article

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

scholarly article

Accurately positioning functional residues with robotics-inspired computational protein design

preprint

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

scientific article

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

scientific article

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

scientific article published on 07 June 2018

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

scientific article published on 21 December 2020

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

scientific article published on 01 March 2020

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

scientific article

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

scientific article

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

scientific article published on 26 September 2016

Biomaterials in non-integer dimensions

scientific article published on 01 July 2019

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

scientific article published on 15 January 2019

Bringing Diffuse X-ray Scattering Into Focus

Bringing diffuse X-ray scattering into focus

scientific article published on 15 February 2018

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

scientific article

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

scientific article published on 23 September 2019

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

scientific article published on 15 October 2020

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

scientific article published on 26 February 2020

Computational design of a modular protein sense-response system

scientific article published on 01 November 2019

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

scientific article

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

scientific article published on January 2017

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

scientific article

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

scientific article published on 04 February 2021

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

scientific article published on 4 February 2016

Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

scientific article

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

scientific article

DNA-binding proteins meet their mismatch

scientific article published on 21 October 2020

Data publication with the structural biology data grid supports live analysis

scientific article

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

scientific article (publication date: 25 April 2016)

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

scientific article published on 21 January 2020

Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins

Diffuse X-ray scattering to model protein motions

scientific article

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

scientific article

Discovery of allosteric binding sites by crystallographic fragment screening

scientific article published on 07 November 2020

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

scientific article

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

scientific article

Effects of α-tubulin acetylation on microtubule structure and stability.

scientific article

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

scientific article published on 23 September 2020

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

scientific article published on 01 August 2020

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

scientific article

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

scientific article published on 23 July 2018

Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin

scientific article published on 12 April 2017

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

Flexible backbone sampling methods to model and design protein alternative conformations

scientific article (publication date: 2013)

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

scientific article published on 24 November 2020

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

scientific article

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

scientific article published on 28 July 2015

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.

scientific article published on 31 August 2016

From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.

scientific article published on 8 August 2013

From systems to structure: bridging networks and mechanism

scientific article

Genetic interaction mapping informs integrative structure determination of protein complexes

scientific article published on 01 December 2020

Hidden alternative structures of proline isomerase essential for catalysis

scientific article

High-density grids for efficient data collection from multiple crystals

scientific article

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

scientific article

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

scientific article published on 9 June 2017

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

scientific article published on 6 April 2006

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

scientific article published on 31 August 2007

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

scientific article

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

scientific article

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

scientific article

Keep on moving: discovering and perturbing the conformational dynamics of enzymes

scientific article

Large language models generate functional protein sequences across diverse families

scientific article from 2023

Ligand binding remodels protein side-chain conformational heterogeneity

scientific article published on 21 March 2022

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

scientific article

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

scientific article published on 01 November 2019

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

scientific article published on 30 September 2015

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

scientific article

Mining electron density for functionally relevant protein polysterism in crystal structures ⬇️

scientific article published on December 29, 2010

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

scientific article published on 04 December 2019

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

scientific article published on 22 May 2015

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

scholarly article published 13 November 2017

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

scientific article published on 15 June 2015

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

scientific article

Preprints for the life sciences ⬇️

scientific article

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

scientific article

Rescue of conformational dynamics in enzyme catalysis by directed evolution.

scientific article

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

scientific article published on 14 February 2022

Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers

scientific article published on 01 August 2019

Synthetic group A streptogramin antibiotics that overcome Vat resistance

scientific article published on 23 September 2020

Systematic functional prioritization of protein posttranslational modifications

scientific article

Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

scientific article published on 16 September 2019

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

scientific article published on 27 May 2022

The tumor-associated EpCAM regulates morphogenetic movements through intracellular signaling.

scientific article

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

scientific article published on 24 February 2020

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

scientific article

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

scientific article published on 18 November 2020

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

scientific article published on 06 December 2018

List of works by James S Fraser

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

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

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

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

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

A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin

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

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

Accurately positioning functional residues with robotics-inspired computational protein design

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

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

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

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

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

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

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

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

Biomaterials in non-integer dimensions

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

Bringing Diffuse X-ray Scattering Into Focus

Bringing diffuse X-ray scattering into focus

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

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

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

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

Computational design of a modular protein sense-response system

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

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

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

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

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

Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

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

DNA-binding proteins meet their mismatch

Data publication with the structural biology data grid supports live analysis

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

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

Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins

Diffuse X-ray scattering to model protein motions

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

Discovery of allosteric binding sites by crystallographic fragment screening

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

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

Effects of α-tubulin acetylation on microtubule structure and stability.

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

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

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

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

Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin

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

Flexible backbone sampling methods to model and design protein alternative conformations

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

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

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

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.

From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.

From systems to structure: bridging networks and mechanism

Genetic interaction mapping informs integrative structure determination of protein complexes

Hidden alternative structures of proline isomerase essential for catalysis

High-density grids for efficient data collection from multiple crystals

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

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

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

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

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

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

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

Keep on moving: discovering and perturbing the conformational dynamics of enzymes

Large language models generate functional protein sequences across diverse families

Ligand binding remodels protein side-chain conformational heterogeneity

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

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

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

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

Mining electron density for functionally relevant protein polysterism in crystal structures ⬇️

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

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

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

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