Skip to Main Content

Author Details

James S Fraser
University of California san francisco
2006
108
43
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37398339Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase.bioRxiv2024
37577651Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain.bioRxiv2024
37425870Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM.bioRxiv2024
36862759Molecular 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.PLoS Pathog2023
37748828Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.Methods Enzymol2023
37651466A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo.PLoS Pathog2023
37535945Chemoenzymatic Syntheses of Fluorine-18-Labeled Disaccharides from [<sup>18</sup>F] FDG Yield Potent Sensors of Living Bacteria <i>In Vivo</i>.J Am Chem Soc2023
37723259Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.Nat Chem2023
37205593Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data.bioRxiv2023
37131711A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis <i>in vivo</i>.bioRxiv2023
37293043Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from [ <sup>18</sup> F]FDG yield potent sensors of living bacteria <i>in vivo</i>.bioRxiv2023
36750095Bacteriophages inhibit and evade cGAS-like immune function in bacteria.Cell2023
36601807Molecular-dynamics simulation methods for macromolecular crystallography.Acta Crystallogr D Struct Biol2023
36702895Large language models generate functional protein sequences across diverse families.Nat Biotechnol2023
35165456Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.Nat Struct Mol Biol2022
35622909The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature.Sci Adv2022
36044899Innate type 2 immunity controls hair follicle commensalism by Demodex mites.Immunity2022
36040268Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data.Protein Sci2022
36240280Ensemble-function relationships to dissect mechanisms of enzyme catalysis.Sci Adv2022
36192635A language model beats alphafold2 on orphans.Nat Biotechnol2022
35254891Accurate positioning of functional residues with robotics-inspired computational protein design.Proc Natl Acad Sci U S A2022
35015630Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.Elife2022
35312477Ligand binding remodels protein side-chain conformational heterogeneity.Elife2022
35149213Integration of software tools for integrative modeling of biomolecular systems.J Struct Biol2022
34931064A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis.Nat Chem Biol2022
35169801The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature.bioRxiv2022
33210433qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps.Protein Sci2021
33853786Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.Sci Adv2021
33542514Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.Nat Methods2021
33860789State of the structure address on MET receptor activation by HGF.Biochem Soc Trans2021
33856343ORACLE reveals a bright future to fight bacteria.Elife2021
34013269CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.bioRxiv2021
34031651CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.Res Sq2021
32353859A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.Nature2020
32090567What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?J Chem Inf Model2020
31930591Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates.Protein Sci2020
31989172Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.Nucleic Acids Res2020
33171388Discovery of allosteric binding sites by crystallographic fragment screening.Curr Opin Struct Biol2020
33376217Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles.Proc Natl Acad Sci U S A2020
33087865DNA-binding proteins meet their mismatch.Nature2020
33060197Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.Science2020
33303586Genetic interaction mapping informs integrative structure determination of protein complexes.Science2020
32968273Synthetic group A streptogramin antibiotics that overcome Vat resistance.Nature2020
32968058Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.Nat Commun2020
32855341Expanding the space of protein geometries by computational design of de novo fold families.Science2020
32148858Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.IUCrJ2020
30645119Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.J Am Chem Soc2019
31754004Computational design of a modular protein sense-response system.Science2019
31867408Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.Struct Dyn2019
31801874Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.Proc Natl Acad Sci U S A2019
  • 1 - 50 of 108

Recommended Authors

Barak Raveh
The Hebrew University of Jerusalem
Career Start Year 2007
Number of shared co-authors 11
Panagiotis L Kastritis
Interdisciplinary Research Center HALOmem, Martin Luther University Halle-Wittenberg
Career Start Year 2007
Number of shared co-authors 9
Abhishek K Jha
Elucidata Corporation
Career Start Year 2005
Number of shared co-authors 1
Sagar D Khare
The State University of New Jersey
Career Start Year 2003
Number of shared co-authors 12
Peter L Freddolino
University of Michigan ann arbor
Career Start Year 2002
Number of shared co-authors 8
Greg L Hura
Lawrence Berkeley National Laboratory, University of California Santa Cruz
Career Start Year 2002
Number of shared co-authors 5
Maya Topf
Leibniz-Institut fur Virologie (LIV)
Career Start Year 2001
Number of shared co-authors 17
Rommie E Amaro
University of California
Career Start Year 2001
Number of shared co-authors 8
Matteo Dal Peraro
Institute of Bioengineering
Career Start Year 2001
Number of shared co-authors 13
Lewyn Li
Dana-Farber Cancer Institute, Harvard Medical School
Career Start Year 2000
Number of shared co-authors 1
Jeffrey B Bonanno
Albert Einstein College of Medicine
Career Start Year 1999
Number of shared co-authors 6
Heather A Carlson
University of Michigan ann arbor
Career Start Year 1999
Number of shared co-authors 1
David R Hall
Diamond Light Source Ltd, Harwell Science & Innovation Campus
Career Start Year 1998
Number of shared co-authors 10
Nikolay V Dokholyan
Pennsylvania State University College of Medicine
Career Start Year 1998
Number of shared co-authors 11
Orly Dym
Weizmann Institute of Science
Career Start Year 1995
Number of shared co-authors 6
Ivet Bahar
Laufer Center for Physical and Quantitative Biology, Stony Brook University
Career Start Year 1994
Number of shared co-authors 7
Giorgio Colombo
Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico
Career Start Year 1993
Number of shared co-authors 6
Tobin R Sosnick
Institute for Biophysical Dynamics, The University of Chicago
Career Start Year 1990
Number of shared co-authors 10
Carlos J Camacho
University of Pittsburgh
Career Start Year 1990
Number of shared co-authors 7
Wladek Minor
University of Virginia
Career Start Year 1989
Number of shared co-authors 12
David Baker
University of Washington
Career Start Year 1988
Number of shared co-authors 50
Ariel Fern??ndez
University of Florida
Career Start Year 1984
Number of shared co-authors 0
Randy J Read
Cambridge Institute for Medical Research, University of Cambridge
Career Start Year 1982
Number of shared co-authors 18
Michal Hammel
Lawrence Berkeley National Laboratory
Career Start Year 1981
Number of shared co-authors 10
Ruth Nussinov
Sackler School of Medicine, Tel Aviv University
Career Start Year 1980
Number of shared co-authors 15
George N Phillips
Rice University
Career Start Year 1974
Number of shared co-authors 14
Charles L Brooks
University of Michigan ann arbor
Career Start Year 1974
Number of shared co-authors 6
Michael Levitt
Stanford University
Career Start Year 1969
Number of shared co-authors 19
Wayne A Hendrickson
Columbia University
Career Start Year 1968
Number of shared co-authors 5
Jens Meiler
Vanderbilt University
Career Start Year 1954
Number of shared co-authors 22

Collaborators

Michael C Thompson
University of California
Co-authored papers 15
Henry van den Bedem
University of California San Francisco
Co-authored papers 14
Tanja Kortemme
University of California san francisco
Co-authored papers 12
Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 11
Iris D Young
University of California san francisco
Co-authored papers 10
Justin T Biel
University of California san francisco
Co-authored papers 9
James M Holton
Lawrence Berkeley National Laboratory
Co-authored papers 9
Michael E Wall
Co-authored papers 8
Paul D Adams
Lawrence Berkeley National Laboratory
Co-authored papers 8
Galen J Correy
University of California san francisco
Co-authored papers 7
Stephanie A Wankowicz
University of California San Francisco
Co-authored papers 7
Natalia Jura
Cardiovascular Research Institute, University of California San Francisco
Co-authored papers 7
Tom Alber
University of California berkeley
Co-authored papers 7
Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 6
Lillian R Kenner
University of California san francisco
Co-authored papers 6
Danielle L Swaney
J. David Gladstone Institutes
Co-authored papers 6
Oren S Rosenberg
University of California san francisco
Co-authored papers 6
Adam Frost
University of California San Francisco
Co-authored papers 5
Yifan Cheng
Quantitative Bioscience Institute, University of California san francisco
Co-authored papers 5
Brian K Shoichet
Department of Pharmaceutical Chemistry, University of California san francisco
Co-authored papers 5
Aashish Manglik
Department of Pharmaceutical Chemistry, University of California San Francisco
Co-authored papers 4
Axel F Brilot
University of California san francisco
Co-authored papers 4
Miles Sasha Dickinson
University of Washington
Co-authored papers 4
Tristan W Owens
University of California san francisco
Co-authored papers 4
David A Agard
University of California, USA Quantitative Biosciences Institute (QBI) san francisco
Co-authored papers 4
Nadia Herrera
University of California san francisco
Co-authored papers 4
Danica Galoni?? Fujimori
University of California San Francisco
Co-authored papers 4
Gregory E Merz
University of California san francisco
Co-authored papers 4
Edmond M Linossi
The Walter and Eliza Hall Institute of Medical Research
Co-authored papers 4
Hannes Braberg
University of California San Francisco
Co-authored papers 4
Release 1.2