Fraser, James S.

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

Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., et al. (2020) · Nature

SARS-CoV-2 and COVID-19 ResearchComputational Drug Discovery Methods

Cited by 4,405

Large language models generate functional protein sequences across diverse families

Madani, A., Krause, B., Greene, E. R., Subramanian, S., Mohr, B. P., Holton, J. M., Olmos, J. L., Xiong, C., Sun, Z. Z., Socher, R., et al. (2023) · Nature Biotechnology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 1,078

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

Barad, B. A., Echols, N., Wang, R. Y.-R., Cheng, Y., DiMaio, F., Adams, P. D., & Fraser, J. S. (2015) · Nature Methods

Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Cited by 886

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

Williams, B. B., Van Benschoten, A. H., Cimermancic, P., Donia, M. S., Zimmermann, M., Taketani, M., Ishihara, A., Kashyap, P. C., Fraser, J. S., & Fischbach, M. A. (2014) · Cell Host & Microbe

Gut microbiota and healthTryptophan and brain disorders

Cited by 732

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

Wang, R. Y.-R., Song, Y., Barad, B. A., Cheng, Y., Fraser, J. S., & DiMaio, F. (2016) · eLife

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 457

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

Fischer, M., Coleman, R. G., Fraser, J. S., & Shoichet, B. K. (2014) · Nature Chemistry

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 149

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

Braberg, H., Jin, H., Moehle, E. A., Chan, Y. A., Wang, S., Shales, M., Benschop, J. J., Morris, J. H., Qiu, C., Hu, F., et al. (2013) · Cell

Genomics and Chromatin DynamicsRNA Research and Splicing

Cited by 143

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

Gupta, M., Azumaya, C. M., Moritz, M., Pourmal, S., Diallo, A., Merz, G. E., Jang, G., Bouhaddou, M., Fossati, A., Brilot, A. F., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory)

SARS-CoV-2 and COVID-19 ResearchAdvanced Electron Microscopy Techniques and Applications

Cited by 89

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

Mavor, D., Barlow, K., Thompson, S., Barad, B. A., Bonny, A. R., Cario, C. L., Gaskins, G., Liu, Z., Deming, L., Axen, S. D., et al. (2016) · eLife

Ubiquitin and proteasome pathwaysEvolution and Genetic Dynamics

Cited by 89

Genetic interaction mapping informs integrative structure determination of protein complexes

Braberg, H., Echeverria, I., Bohn, S., Cimermancic, P., Shiver, A., Alexander, R., Xu, J., Shales, M., Dronamraju, R., Jiang, S., et al. (2020) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 37

Automated multiconformer model building for X-ray crystallography and cryo-EM

Wankowicz, S. A., Ravikumar, A., Sharma, S., Riley, B., Raju, A., Hogan, D. W., Flowers, J., van den Bedem, H., Keedy, D. A., & Fraser, J. S. (2024) · eLife

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 28

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

Estevam, G. O., Linossi, E. M., Macdonald, C. B., Espinoza, C. A., Michaud, J. M., Coyote-Maestas, W., Collisson, E. A., Jura, N., & Fraser, J. S. (2024) · eLife

Lung Cancer Treatments and MutationsCancer Genomics and Diagnostics

Cited by 22

Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning

Estevam, G. O., Linossi, E., Rao, J., Macdonald, C. B., Ravikumar, A., Chrispens, K. M., Capra, J. A., Coyote-Maestas, W., Pimentel, H., Collisson, E. A., et al. (2025) · eLife

Lung Cancer Treatments and MutationsCancer Genomics and Diagnostics

Cited by 17

Of Problems and Opportunities – How to Treat and How to Not Treat Crystallographic Fragment-Screening Data

Weiss, M. S., Wollenhaupt, J., Correy, G. J., Fraser, J. S., Heine, A., Klebe, G., Krojer, T., Thunnissen, M., & Pearce, N. M. (2022) · Protein Science

Enzyme Structure and FunctionCrystal structures of chemical compounds

Cited by 13

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

Weiss, M. S., Wollenhaupt, J., Correy, G. J., Fraser, J. S., Heine, A., Klebe, G., Krojer, T., Thunissen, M., & Pearce, N. M. (2022) · Protein Science

Enzyme Structure and FunctionCrystal structures of chemical compounds

Cited by 13

Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning

Estevam, G. O., Linossi, E., Rao, J., Macdonald, C. B., Ravikumar, A., Chrispens, K. M., Capra, J. A., Coyote-Maestas, W., Pimentel, H., Collisson, E. A., et al. (2025) · eLife

Lung Cancer Treatments and MutationsCancer Genomics and Diagnostics

Cited by 6

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

Chen, D. F., Roe, L. T., Li, Y., Borges, A. L., Zhang, J. Y., Babbar, P., Maji, S., Stevens, M. G. V., Correy, G. J., Diolaiti, M. E., et al. (2024) · mBio

CRISPR and Genetic EngineeringBacteriophages and microbial interactions

Cited by 4

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

Chen, D. F., Roe, L. T., Yuping, L., Borges, A. L., Zhang, J. Y., Babbar, P., Maji, S., Stevens, M. G. V., Correy, G. J., Diolaiti, M. E., et al. (2025) · mBio

CRISPR and Genetic EngineeringBacteriophages and microbial interactions

Cited by 4