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James S. Fraser

Professor, University of California San Francisco
在 ucsf.edu 的電子郵件地址已通過驗證
被引用 16359 次

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

H Van Den Bedem, JS Fraser - Nature methods, 2015 - nature.com
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to
interact with binding partners or perform the chemical reactions required for a multitude of …

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

DE Gordon, GM Jang, M Bouhaddou, J Xu, K Obernier… - Nature, 2020 - nature.com
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has …

Large language models generate functional protein sequences across diverse families

A Madani, B Krause, ER Greene, S Subramanian… - Nature …, 2023 - nature.com
Deep-learning language models have shown promise in various biotechnological
applications, including protein design and engineering. Here we describe ProGen, a …

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

JS Fraser, KL Maxwell, AR Davidson - Current opinion in microbiology, 2007 - Elsevier
Recent work has shown that Immunoglobulin-like (Ig-like) domains occur frequently on the
surface of tailed dsDNA bacteriophages. Several of these Ig-like domains are added to …

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

BA Barad, N Echols, RYR Wang, Y Cheng, F DiMaio… - Nature …, 2015 - nature.com
Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of
validation metrics to independently assess map quality and model geometry. We report …

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

G Bhabha, JT Biel, JS Fraser - Accounts of chemical research, 2015 - ACS Publications
Conspectus Because living organisms are in constant motion, the word “dynamics” can hold
many meanings to biologists. Here we focus specifically on the conformational changes that …

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

JS Fraser, H Van Den Bedem… - Proceedings of the …, 2011 - National Acad Sciences
Modern protein crystal structures are based nearly exclusively on X-ray data collected at
cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little …

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

BB Williams, AH Van Benschoten, P Cimermancic… - Cell host & …, 2014 - cell.com
Several recent studies describe the influence of the gut microbiota on host brain and
behavior. However, the mechanisms responsible for microbiota-nervous system interactions …

Hidden alternative structures of proline isomerase essential for catalysis

JS Fraser, MW Clarkson, SC Degnan, R Erion, D Kern… - Nature, 2009 - nature.com
A long-standing challenge is to understand at the atomic level how protein dynamics
contribute to enzyme catalysis. X-ray crystallography can provide snapshots of …

[HTML][HTML] Systematic functional prioritization of protein posttranslational modifications

P Beltrao, V Albanèse, LR Kenner, DL Swaney… - Cell, 2012 - cell.com
Protein function is often regulated by posttranslational modifications (PTMs), and recent
advances in mass spectrometry have resulted in an exponential increase in PTM …