Ray Berkeley

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RAYMOND BERKELEY

Department of Chemistry, Scripps Research

10550 N. Torrey Pines Rd., La Jolla, CA 92037

RESEARCH EXPERIENCE

Scripps Research, La Jolla, CA February 2025 - Present
Advisor: Benjamin F. Cravatt III
Structural bioinformatic approaches to characterizing the non-orthosteric ligandable proteome; structural and chemical proteomic characterization of covalent modulators of protein-protein interactions.

University of California, San Diego, La Jolla, CA July 2023 - February 2025
Advisor: Mark A. Herzik Jr.
Development of machine learning applications for particle curation in cryoEM data.

University of California, San Diego, La Jolla, CA September 2017 - July 2023
Advisor: Galia T. Debelouchina
Characterization of the physical and biochemical basis of protein phase transitions using chemical, structural, and computational biology methods.

University of California, Santa Cruz, Santa Cruz, CA August 2012 - November 2015
Advisor: R. Scott Lokey
Investigation of the chemical basis for the passive permeability of cyclic peptide macrocycles; determination of the mechanism of action of a bioactive small molecule by whole genome sequencing of resistant mutants.

University of Oxford, Oxfordshire, UK January 2015 - March 2015
Advisor: Stuart J. Conway
Synthesis of analogs of a dimethylisoxazole-based bromodomain inhibitor.

PROFESSIONAL EXPERIENCE

Bioinformatics Programmer II July 2023 - February 2025
University of California, San Diego, La Jolla, CA
Advisor: Mark A. Herzik Jr.
Development of machine learning applications for particle curation in cryoEM data.

Research Associate, Chemistry November 2015 - August 2017
Mendel Biological Solutions, Hayward, CA
Advisors: Peter P. Repetti & Joshua I. Armstrong
Discovery and development of bioactive natural products for the enhancement of crop performance in agriculture.

EDUCATION

University of California, San Diego
Ph.D., Chemical Biology, 2023

University of California, Santa Cruz
B.S., Molecular, Cell, & Developmental Biology with a minor in Bioinformatics, 2015

PUBLICATIONS

9.: Hayward, R.E., Berkeley, R.F., Gao, Z., Garhammer, M., Morizono, M.A., Njomen, E., … Melillo, B., Cravatt, B.F. (2025). Tryptoline stereoprobe elaboration identifies inhibitors of the grpel1-hspa9 chaperone complex. bioRxiv. ( link, pdf)
8.: Berkeley, R.F.*, Cook, B.C.*, Ji, D., Foroughi, A., Saladi, A., Bachochin, M., & Herzik Jr., M.A. (2025). Removal of false particle images from cryoEM data using ANTIDOTE: A Neural network Trained In Deleterious ObjecT Elimination. bioRxiv. ( link, pdf)
7.: Berkeley, R.F.*, Plonski, A.P.*, Phan, T.M.*, Grohe, K., Becker, L., Wegner, S., … Mittal, J., Debelouchina, G.T. (2025). Capturing the conformational heterogeneity of HSPB1 chaperone oligomers at atomic resolution. J. Am. Chem. Soc., 147(18), 15181–15194. ( link, pdf)
6.: Berkeley, R.F.*, Cook, B.C.*, & Herzik Jr., M. (2024). Machine learning approaches to density modification improve map quality at the cost of ligand density quality. Front. Mol. Biosci., 11, 1404885. ( link)
5.: Berkeley, R.F., & Debelouchina, G.T. (2022). Chemical tools for study and modulation of biomolecular phase transitions. Chem. Sci., 13(48), 14226–14245. ( link, pdf)
4.: Berkeley, R.F., Kashefi, M., & Debelouchina, G.T. (2021). Real-time observation of structure and dynamics during the liquid-to-solid transition of FUS LC. Biophys. J., 120(7), 1276–1287. ( link, pdf)
3.: Lim, B. J., Berkeley, R.F., & Debelouchina, G.T. (2020). Fused split inteins: Tools for introducing multiple protein modifications. In Methods mol. biol. (Vol. 2133, pp. 163–181). New York, NY: Humana. ( link)
2.: Schwochert, J., Turner, R., Thang, M., Berkeley, R.F., Ponkey, A. R., Rodriguez, K. M., … Lokey, R.S (2015). Peptide to peptoid substitutions increase cell permeability in cyclic hexapeptides. Org. Lett., 17(12), 2928–2931. ( link, pdf)
1.: Wride, D.A., Pourmand, N., Bray, W.M., Kosarchuk, J., Nisam, S., Quan, T., … Lokey, R.S. (2014). Confirmation of the cellular targets of benomyl and rapamycin using next-generation sequencing of resistant mutants in S. cerevisiae. Mol. BioSyst., 10(12), 3179–3187. ( link, pdf)
* equal contribution

AWARDS AND HONORS

2022ACS Graduate Student and Postdoctoral Scholar Recognition Program Award for Leadership in Mentoring

2021Bruno Zimm Award

2019–2020San Diego Fellowship*

2018–2020NIH Chemistry-Biology Interface Predoctoral Training Program*

* full support

SERVICE

: 2023Global NMR Twitter Conference Judge

2022ACSSA Undergraduate Research Symposium Judge

2021Debelouchina Lab UCSD Mentor-Mentee Workshop

2021Mira Mesa High School ScienceBridge Program Speaker

2021ACSSA Undergraduate Research Symposium Moderator

2020UCSD Grad Pals Mentorship Program

2018–2020ChemPAL Mentorship Program

2012Juvenile Diabetes Research Foundation Counsellor

INVITED AND CONTRIBUTED TALKS

: 2023San Diego cryoEM Supergroup, La Jolla, CA

2023Biophysical Society Annual Meeting (IDP subgroup early career speaker), San Diego, CA

2022UT Southwestern Biophysics Seminar Series (lightning talk), Dallas, TX

2022International Council on Magnetic Resonance in Biological Systems (lightning talk), Boston, MA

2021UCSD Graduate Student Seminar Series, Virtual

2021San Diego NMR Supergroup, Virtual

2021San Diego Python Users Group, Virtual

2019Chemistry Biology Interfaces Symposium, UC San Diego, La Jolla, CA

2019CBI-CRIN Industry Interaction Day (Lightning Talk), UC San Diego, La Jolla, CA

2018Chemistry Biology Interfaces Symposium, UC San Diego, La Jolla, CA