Woonghee Lee

Woonghee Lee
Assistant Professor
Department of Chemistry

Mailing Address:
Department of Chemistry
Campus Box 194, P.O. Box 173364
Denver, CO 80217-3364

Office Location:
Science Building
Room 4128A

Group webpage: https://poky.clas.ucdenver.edu/wlee-group
Poky suite webpage: https://poky.clas.ucdenver.edu

Expertise Areas:

Biomolecular NMR, Protein Structure and Function, Integrative Structural Biology, Infectious Disease, AI/ML, Automated NMR Analysis, Integrated Software, Big Data

Education & Degrees:

Ph.D., Biochemistry, University of Wisconsin-Madison, 2013 (Prof. John Markley’s group)

M.S., Biochemistry, Yonsei University, 2008 (Prof. Weontae Lee’s group)

B.S., Biochemistry, Yonsei University, 2006

I.E.I.P., Human Resources Development Service of Korea (National IT Specialist since 2000)


Before joining our department, Prof. Woonghee Lee was a principal investigator and a staff scientist at National Magnetic Resonance Facility At Madison (NMRFAM) developing automation algorithms and building an integrated software platform for efficient and easy-to-use NMR-based protein structure analysis through `full-stack development.’ He is a developer of the popular analytic software tools such as NMRFAM-SPARKY, I-PINE, PONDEROSA-C/S, PACSY, etc and majority of them are considered the `field standards.’ Much of his skill in innovation stems from three years of experience as a programmer at a geographical information system (GIS) software development company that fulfilled his military service (EnGIS technologies). He is also an author of many Protein Data Bank (PDB) and Biological Magnetic Resonance Bank (BMRB) entries related to the common cold, Ebola, Wilson’s disease, protein folding mechanisms, etc.

Prof. W. Lee’s group in the Department of Chemistry at University of Colorado Denver focuses on the development and application of computational and experimental research methods geared toward human well-being. His group members combine expertise as biochemists with software development skills, and they are eager to contributing indispensable high-throughput tools for analyzing biochemical/biophysical data and making technological breakthroughs towards a better understanding of protein 3D structures in terms of their roles and behaviors in biological context. He always welcomes and enjoys talking to self-motivated researchers in every level including undergrads. He was an undergraduate research scholars (URS) program mentor at University of Wisconsin-Madison before coming to University of Colorado Denver.

Selected Publications:

  1. Shao H, Boulton S, Olivieri C, Mohammed H, Akimoto M, Subrahmanian M, Veglia G, Markley J, Melacini G, Lee W*. CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. Bioinformatics. 2020; epub. https://doi.org/10.1093/bioinformatics/btaa781
  2. Weber DK, Wang S, Markley JL, Veglia G, Lee W*. PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. Bioinformatics. 2020; 36:9:2915-6.
  3. Lee W*, Bahrami A, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Markley JL. I-PINE web server: an integrative probabilistic NMR assignment system for proteins. Journal of Biomolecular NMR. 2019 May;73(5):212-222.
  4. Lee W*, Markley JL. PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinformatics 2018 May 1; 34(9): 1586-1588.
  5. Yu CH†, Lee W†, Nokhrin S, Dmitriev OY. (equally contributed first authors) The Structure of Metal Binding Domain 1 of the Copper Transporter ATP7B Reveals Mechanism of a Singular Wilson Disease Mutation. Scientific Reports 2018 Jan 12; 8(1): 581.
  6. Lee W*, Petit CM, Cornilescu G, Stark JL, Markley JL. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. Journal of Biomolecular NMR. 2016 June; 65(2): 51-57.
  7. Lee W*, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Wildman-Henzler K, Markley JL. Integrative NMR for biomolecular research. Journal of Biomolecular NMR. 2016 Apr; 64(4): 307-332. – F1000Prime
  8. Lee W*, Tonelli M, Markley JL. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 2015 Apr; 31(8): 1325-1327.
  9. Lee W*, Stark JL, Markley JL. PONDEROSA-C/S: Client-server based software package for automated protein 3D structure determination. Journal of Biomolecular NMR 2014 Nov; 60(2-3): 73-75.
  10. Lee W, Watters KE, Troupis AT, Reinin NM, Suchy FP, Moyer K, Frederick RO, Tonelli M, Aceti DJ, Palmenberg AC, Markley JL. Solution structure of the 2A protease from a common cold agent, human rhinovirus C2, strain W12. PLoS ONE. 2014 June 17; 9(6): e97198.

Courses Taught:

Regular Courses

Physical Chemistry Laboratory II (CHEM 4538, CU Denver Fall 2021)

Instrumental Analysis Laboratory (CHEM 4128), CU Denver Spring 2021)

Directed Research (CHEM 4880, CU Denver Spring 2021, Fall 2021)

Biochemical Methods Laboratory (BIOCHEM 651, TA at UW-Madison Spring 2011)

Junior Seminar (BCH 2001, TA at Yonsei University Fall 2007)

Biophysical Chemistry (BCH 3103, TA at Yonsei University Spring 2007)


NMRFAM Protein Structure Determination Workshop (Instructor at NMRFAM Summer 2009 – Summer 2021)

NMRFAM Advanced Structure Refinement Workshop (Instructor at NMRFAM Summer 2014 – Summer 2015)

NMRbox Summer Workshop Series “Biomolecular NMR Automation and Its Application” (1-day organizer on Zoom, Aug. 4, 2020)

NMRFAM Remote Workshops (Instructor; Seoul Nat’l University, Yonsei University, Konkuk University, Gyeonsang Nat’l University Summer 2016 – Spring 2017)

Guest Lectures

Biochemical Application of NMR (BIOCHEM 801, Guest Lecture at UW-Madison Spring 2013 – Spring 2020)

Physical Chemistry (Guest Lecture at Gyeongsang Nat’l University Spring 2017)