Publications

60. Giraldo AEL, Rahimi M, Lee W*. 

Method to use chemical shift predictors in protein NMR assignments.

In preparation.

59. Seong H, Lee J, Park JK, Lee W, Seo J, Choi J. 

Redox-Active Tungsten Mono-Oxo Bis(dithiolene) Complex: A Fast-Rechargeable Anode for High-Capacity Lithium-Ion Batteries.

Submitted.

58. Chiu A, Lee W*. 

Modernizing Biomolecular NMR: the POKY suite.

In revision.

57. Kim HI, Boo M, Chiu A, K H-L, K D-H, Sim JO, Han Y, Park WY, Cheon C, Lee I-S, Kim K-I, Jung JH, Kim W, Um J-Y, Lee W, Otterbein LE, Park J, Ko S-G. 

A novel herbal formula derived from Danggui Bohyul Tang enhances cisplatin efficacy by inhibiting neutrophil extracellular trap formation in lung cancer.

Submitted

56. Dag C, Kazar AE, Kahraman K, Gocenler O, Lee W, Lambert M, Ceylan CDT, Shim JG, Haas AL, Dotsch V, Ziarek JJ, Elgin ES .

Role of Uba7-UFD in E1-E2 ISGylation: NMR-Based Insights into E2 Binding Dynamics .

In Revision.

55. Jin Y, Seong H, Moon JH, Kim G, Jang JY, Lee JB, Kwon S-R, Lee W, Lee K-T, Choi J.

Unraveling the High-Rate Electrochemical Kinetics of CuSbS2 for Sodium Storage.

Submitted.

54. Ma Q, Huang J, Boulton S, Mak E, Akimoto M, Giraldo AEL, Truong M, Daka M, Huynh A, Clare R, Kwok S, Nazy I, Lee W, Melacini G. 

Resonance Assignments of Asymmetric Tetrameric Platelet Factor 4 (PF4).

Biomolecular NMR Assignments. epub. https://doi.org/10.1007/s12104-025-10246-1

53. Mun H, Choi K-M, Fei Q, Giraldo AEL, Lee JW, Kim K, Min K-W, Shi L, Bedford MT, Kim D-C, Chun YL, Ryu S, Kim D, Chang JH, Kang S-U, Lee W*, Yoon J-H.

SARS-CoV-2 RNA-binding protein suppresses extracellular miRNA release.

RNA Biology. 2025 Dec; 22(1):1-17. https://doi.org/10.1080/15476286.2025.2527494

52. Giraldo AEL, Rahimi M, Lee W*.

Automated Chemical Shift Assignments of MAS Solid-State NMR Spectra of Complex Protein Systems by ssPINE/ssPINE-POKY.

Appl. Sci. 2025; 15(12); 6563. https://doi.org/10.3390/app15126563

51. Seong H, Moon JH, Jin Y, Kim G, Jung T, Yoo H, Lee W, Lee K, Cho SY, Choi J. 

Redox-active Co(II) and Zn(II) Pincer Complexes as High-capacity Anode Materials for Lithium-ion Batteries.

Advanced Science. 2025; 12; 2413656. https://doi.org/10.1002/advs.202413656

50. Jin Y, Yoo H, Seong H, Moon JH,Kim G, Jung T, Myung Y, Lee W, Kim S, Choi J. 

Cubic Cu3SnS4@CNT for Stable and High-Temperature Sodium-Ion Batteries: Simple Colloidal Synthesis and Enhanced Cycle Performance.

Chemical Engineering Journal. 2025; 503; 158461. https://doi.org/10.1016/j.cej.2024.158461

49. Chiu A, Rahimi M, Lee W*.

A-SIMA/A-MAP: A Comprehensive Toolkit for NMR-based Metabolomics Analysis.

Metabolomics. 2025; 21:10. https://doi.org/10.1007/s11306-024-02208-w

48. Rahimi M†, Chiu A†, Giraldo AEL, Yoon J-H, Lee W*. (†equally contributed first authors)

REDEN: Interactive Multi-Fitting Decomposition-based NMR Peaks Picking Assistant.

Journal of Magnetic Resonance. 2024 Jan; 358:107600. https://doi.org/10.1016/j.jmr.2023.107600

47. Wi S, Li C, Pham K, Lee W, Frydman L. 

Short and long range 2D 15N-15N NMR correlations among peptide groups by novel solid state dipolar mixing schemes.

Journal of Biomolecular NMR. 2024 Mar; 78:19-30. https://doi.org/10.1007/s10858-023-00429-0

46. Giraldo AEL, Werner Z, Rahimi M, Lee W*. 

Breaking Boundaries: TINTO in POKY for Computer Vision-Based NMR Walking Strategies.

Journal of Biomolecular NMR. 2023 Dec; 77:217-228. https://doi.org/10.1007/s10858-023-00423-6

45. Kaifeng Hu†, Woonghee Lee†,*, Gaetano T. Montelione†, Nikolaos G. Sgourakis†, Beat Vögeli†. (†equally contributed first authors)

Editorial: Computational Approaches for Interpreting Experimental Data and Understanding Protein Structure, Dynamics and Function Relationships.

Front. Mol. Biosci., 03 October 2022. Sec. Structural Biology. https://doi.org/10.3389/fmolb.2022.1018149

44. Manthey I, Tonelli M, Clos II L, Rahimi M, Markley JL, Lee W*. 

POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data.

Journal of Structural Biology: X. 2022 Aug 28; 6:100073. https://doi.org/10.1016/j.yjsbx.2022.100073

43. Dwarasala A, Rahimi M, Markley JL, Lee W*. 

ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR from Complex Protein Systems.

Membranes. 2022; 12(9): 834. Special Issue: Advanced Research on Structure-Function Relationships of Membrane Proteins (Vol II). https://doi.org/10.3390/membranes12090834

42. Rahimi M, Lee Y, Nguyen H, Chiu A, Lee W*. 

A Toolset for the Solid-state NMR-based 3D Structure Calculation of Proteins.

Journal of Magnetic Resonance. 2022 June; 339:107214. https://doi.org/10.1016/j.jmr.2022.107214

41. Yang MJ, Kim J, Lee Y, Lee W*, Park CJ. 

NMR Structure and Biophysical Characterization of Thermophilic Single-stranded DNA Binding Protein from Sulfolobus solfataricus.

International Journal of Molecular Sciences. 2022; 23(6):3099. https://doi.org/10.3390/ijms23063099

40. Smith K†, Lee W†, Tonelli M, Lee Y, Light S, Cornilescu G, Chakravarthy S. (†equally contributed first authors) 

Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach.

Protein Science. 2022 May; 31(5):e4282. https://doi.org/10.1002/pro.4282

39. Roy S†, Boral S†, Maiti S, Kushwaha T, Basak AJ, Lee W, Basak A, Gholap SL, Inampudi KK, De S. (†equally contributed first authors) 

Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition.

FEBS Journal. 2022 May; 289(10):2847-2864. https://doi.org/10.1111/febs.16301

38. Lee Y†, Tonelli M†, Rahimi M, Anderson KT,  Kirchdoerfer RN, Henzler-Wildman K, Lee W*. (†equally contributed first authors) 

pH-dependent polymorphism of the structure of SARS-CoV-2 nsp7.

bioRxiv. https://doi.org/10.1101/2021.09.10.459800 

37. Uhlemann EE†, Lee W†, Tonelli M, Dmitriev OY. (†equally contributed first authors) 

At sixes and sevens: a cryptic domain in the metal binding chain of the human copper transporter ATP7A.

Biophysical Journal. 2021 Oct 19; 120(20):4600-4607. https://doi.org/10.1016/j.bpj.2021.08.029 

Highlighted as a "New and Notable" item from the journal. 

36. Lee W*, Rahimi M, Lee Y, Chiu A.

POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules.

Bioinformatics. 2021 Sep. 15; 37(18):3041-3042. https://doi.org/10.1093/bioinformatics/btab180

35. Rahimi M, Lee Y, Markley JL, Lee W*.

iPick: Multiprocessing Software for Integrated NMR Signal Detection and Validation.

Journal of Magnetic Resonance. 2021 July; 328:106995. https://doi.org/10.1016/j.jmr.2021.106995

34. Shao H, Boulton S, Olivieri C, Mohamed H, Akimoto M, Subrahmanian MV, Vegilia G, Markley JL, Melacini G, Lee W*.

CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery.

Bioinformatics. 2021 Apr. 15; 37(8):1176-77. http://doi.org/10.1093/bioinformatics/btaa781

33. Yang MJ, Lee W*, Park CJ.

Resonance assignments and secondary structure of thermophile single-stranded DNA binding protein from Sulfolobus solfataricus at 323K.

Biomolecular NMR Assignments. 2021 Apr. 15:159-164. https://doi.org/10.1007/s12104-020-09999-8

32. Lee W, Fredrick R, Tonelli M, Palmenberg AC.

Solution NMR Determination of the CDHR3 Rhinovirus-C Binding Domain, EC1.

Viruses. 2021; 13(2):159. Special Issue: Rhinovirus Infections. https://doi.org/10.3390/v13020159

31. Chen CY, Lee W, Renhowe P, Jung J, Montfort WR.

Solution structures of the Shewanella woodyi H-NOX protein in the presence and absence of soluble guanylyl cyclase stimulator IWP-051.

Protein Science. 2021; 30:448-463. https://doi.org/10.1002/pro.4005

Previously deposited in bioRxiv. 2020 Aug. 23. https://doi.org/10.1101/2020.08.21.262071

30. Boral S, Maiti S, Basak AJ, Lee W, De S. 

Structural, dynamic and functional characterization of a new DnaX mini intein derived from Spirulina platensis provides new insights into intein-mediated catalysis of protein splicing. 

Biochemistry. 2020 Dec 8; 59(50):4711-4724. https://doi.org/10.1021/acs.biochem.0c00828

29. Basak AJ, Maiti S, Hansda A, Mahata D, Duraivelan K, Kundapura SV, Lee W, Mukherjee G, De S, Samanta D.

Structural insights into N-terminal IgV domain of BTNL2, a T cell inhibitory molecule, suggests a non-canonical binding interface for its putative receptors

Journal of Molecular Biology. 2020 Nov; 432(22):5938-5950. https://doi.org/10.1016/j.jmb.2020.09.013

28. Weber KD, 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 May; 36(9):2915-2916. https://doi.org/10.1093/bioinformatics/btaa019

27. Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. 

Solution structure of human myeloid-derived growth factor, a prototype of the widespread MYDGF proteins. 

Nature Communications. 2019;10:5612. https://doi.org/10.1038/s41467-019-13577-5

26. Lee W, Tonelli M, Wu C, Aceti D, Amarasinghe GK, Markley JL. 

Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600-739 construct. 

Biomolecular NMR Assignments. 2019 Oct;13(2):315-319. https://doi.org/10.1007/s12104-019-09898-7

25. 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. https://doi.org/10.1007/s10858-019-00255-3

24. Shrestha OK, Sharma R, Tomiczek B, Lee W, Tonelli M, Cornilescu G, Stolarska M, Lukasz N, Czub J, Markley JL, Marszalek J, Ciesielski SJ, Craig EA. 

Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70. 

PLoS One. 2019 May 15; 14(5):e0217098. https://doi.org/10.1371/journal.pone.0217098

23. Frederick RO, Haruta M, Tonelli M, Lee W, Cornilescu G, Cornilescu C, Sussman MR, Markley JL. 

Function and solution structure of the arabidopsis thaliana RALF8 peptide. 

Protein Science. 2019 Jun;28(6):1115-1126. https://doi.org/10.1002/pro.3628

22. Lee W*, Markley JL. 

PINE-SPARKY.2 for automated NMR-based protein structure research. 

Bioinformatics 2018 May 1; 34(9): 1586-1588. https://doi.org/10.1093/bioinformatics/btx785

21. 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. https://doi.org/10.1038/s41598-017-18951-1

20. Schilke BA, Ciesielski SJ, Ziegelhoffer T, Tonelli M, Lee W, Cornilescu G, Markley JL, Craig EA.

Broadening the functionality of a J-protein/Hsp70 molecular chaperone system. 

PLoS Genetics 2017 Oct 30; 13(10):e1007084. https://doi.org/10.1371/journal.pgen.1007084

19. 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. https://doi.org/10.1007/s10858-016-0036-y

18. 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. https://doi.org/10.1007/s10858-016-0029-x

17. Stark JL, Eghbalnia H, Lee W, Westler WM, Markley JL. 

NMRmix: a tool for the optimization of compound mixtures for 1D 1H NMR ligand affinity screens. 

Journal of Proteome Research 2016 April; 15(4): 1360-1368. https://doi.org/10.1021/acs.jproteome.6b00121

16. Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL. 

Probabilistic validation of protein NMR chemical shift assignments. 

Journal of Biomolecular NMR 2016 Jan; 64(1):17-25. https://doi.org/10.1007/s10858-015-0007-8

15. Dashti H, Lee W, Tonelli M, Cornilescu CC, Assadi-Porter FM, Westler WM, Eghbalnia HR, Markley JL. 

NMRFAM-SDF: a protein structure determination framework. 

Journal of Biomolecular NMR 2015 Aug; 62(4): 481-495. https://doi.org/10.1007/s10858-015-9933-8

14. Lee W*, Tonelli M, Markley JL. 

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. 

Bioinformatics 2015 Apr; 31(8): 1325-1327 – The highly cited paper (Web of Science). https://doi.org/10.1093/bioinformatics/btu830

13. Tonelli M, Eller CH, Singarapu KK, Lee W, Bahrami A, Westler WM, Raines RT, Markley JL.

Assignments of RNase A by ADAPT-NMR and enhancer. 

Biomolecular NMR Assignments. 2015 Apr 1; 9(1): 81-88. https://doi.org/10.1007/s12104-014-9549-z

12. 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. https://doi.org/10.1007/s10858-014-9855-x

11. Baßler J, Paternoga H, Holdermann I, Thoms M, Granneman S, Barrio-Garcia C, Nyarko A, Lee W, Stier G, Clark SA, Schraivogel D, Kallas M, Beckmann R, Tollervey D, Barbar E, Sinning I, Hurt E. 

A network assembly factors is involved in remodeling rRNA elements during preribosome maturation. 

Journal of Cell Biology 2014 Nov 24; 207(4): 481-498. https://doi.org/10.1083/jcb.201408111

Featured in a issue: A molecular chain gang at work in maturing ribosomes. 

Journal of Cell Biology 2014 Nov 24; 207(4): 435. https://doi.org/10.1083/jcb.2074if

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. https://doi.org/10.1371/journal.pone.0097198

9. Poplawski A, Hu K, Lee W, Peng D, Carlson S, Shi X, Markley JL, Glass KC. 

Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. 

Journal of Molecular Biology. 2014 Apr 17; 426(8): 1661-1676. https://doi.org/10.1016/j.jmb.2013.12.007

8. Lee W†,*, Hu K†, Tonelli M, Bahrami A, Neuhardt E, Glass KC, Markley JL. (†equally contributed first authors) 

Fast automated NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers. 

Journal of Magnetic Resonance. 2013 Aug 30; 236C: 83-88 – F1000Prime. https://doi.org/10.1016/j.jmr.2013.08.010

7. Lee W*, Bahrami A, Markley JL. 

ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. 

Bioinformatics. 2013 Feb 15; 29(4): 515-7. https://doi.org/10.1093/bioinformatics/bts692

6. Lee W*, Yu W, Kim S, Chang I, Lee W, Markley JL. 

PACSY, a relational database management system for protein structure and chemical shift analysis. 

Journal of Biomolecular NMR. 2012 Oct; 54(2): 169-179. https://doi.org/10.1007/s10858-012-9660-3

5. Yu W, Lee W, Lee W, Kim S, Chang I. 

Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids. 

Journal of Biomolecular NMR. 2011 Dec; 51(4): 411-24. https://doi.org/10.1007/s10858-011-9579-0

4. Lee W*, Kim JH, Westler WM, Markley JL. 

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. 

Bioinformatics. 2011 Jun 15; 27(12): 1727-8. https://doi.org/10.1093/bioinformatics/btr200

3. Lee W*, Westler WM, Bahrami A, Eghbalnia HR, Markley JL. 

PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. 

Bioinformatics. 2009 Aug 15; 25(16): 2085-7. https://doi.org/10.1093/bioinformatics/btp345

2. Shin J, Lee W, Lee W. 

Structural proteomics by NMR spectroscopy. 

Expert Review of Proteomics. 2008 Aug; 5(4): 589-601. https://doi.org/10.1586/14789450.5.4.589

1. Kwak S, Lee W, Shin J, Ko S, Lee W. 

Purification and backbone assignment of the Hypothetical Protein MTH1821 from Methanobacterium thermoautotrophicum H. 

Journal of the Korean Magnetic Resonance Society. 2007 Jan; 11: 73-84. http://www.koreascience.or.kr/article/ArticleFullRecord.jsp?cn=JGGMB2_2007_v11n2_73

* denotes (co-)corresponding authorship.

Complete List of Published Work in Woonghee Lee's Bibliography

https://www.ncbi.nlm.nih.gov/myncbi/woonghee.lee.1/bibliography/public/

Patents

2. Lee W, Lee W. Method to predict protein secondary structure using NMR spectroscopy. KR Patent #1008899400000. https://doi.org/10.8080/1008899400000

1. Lee W, Lee W. Prediction method of protein 3-dimensional structure using automated peak searching, apparatus and recording medium. KR Patent #1009509670000. https://doi.org/10.8080/1020080008752