Publication List

(underlined names are graduate students and italicized names are undergraduates mentored by the PI)

31. Li R, Stevens CA, Cho SS. Molecular dynamics simulations of protein-nanoparticle biocorona formation. Modeling, Methodologies and Tools for Molecular and Nano-scale Communications, Eds. Junichi Suzuki, Tadashi Nakano, Michael J. Moore, 2015, Springer Publishing. (in press)
30. Li R, Macnamara, LM, Leuchter JD, Alexander RW, Cho SS. MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery. International Journal of Molecular Sciences, Special Issue: Functions of Transfer RNA, 2015, 16:15872-15902.
29. Burg J, Pauca VP, Turkett W, Fulp E, Cho SS, Santago P, Cañas D, Gage HD. Engaging Non-Traditional Students in Computer Science through Socially-Inspired Learning and Sustained Mentoring. Proceedings of the 46th ACM Technical Symposium on Computer Science Education, 2015, 639-644 (36% acceptance rate).
28. Leuchter JD, Green AT, Gilyard J, Rambarat CG, Cho SS. Coarse-grained and atomistic MD simulations of RNA and DNA folding. Israel J. Chem. Special Issue: 2013 Nobel Prize in Chemistry: Computational Chemistry of Biomolecules, 2014, 54: 1152–1164.
27. Cho SS, Pauca VP, Johnson D, James Y. Computational Thinking for the Rest of Us: A Liberal Arts Approach to Engaging Middle and High School Teachers with Computer Science Students. Proceedings of the Society for Information Technology and Teacher Education, 2014.
26. Li R, Chen R, Chen P, Wen Y, Ke P, Cho SS. Computational and experimental characterizations of silver nanoparticle-apolipoprotein biocorona. J. Phys. Chem. B, 2013, 117, 13451-13456.
25. Proctor AJ, Stevens CA, Cho SS. GPU-optimized hybrid neighbor/cell list algorithm for coarse-grained MD simulations of protein and RNA folding and assembly. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2013, 633-640. (29% acceptance rate)
24. Li R, Ge H, Cho SS. Sequence-dependent base stacking interactions guide tRNA folding energy landscapes. J. Phys. Chem. B, 2013, 117, 12943-12952.
23. Proctor AJ, Lipscomb TJ, Zou A, Anderson AJ, Cho SS. GPU-optimized coarse-grained MD simulations of protein and RNA folding and assembly. ASE Science Journal, 2012, 1, 1-11. (3.9% acceptance rate)
22. Proctor AJ, Lipscomb TJ, Zou A, Anderson AJ, Cho SS. Performance analyses of a parallel Verlet neighbor list algorithm for GPU-optimized MD simulations. Proceedings of the ASE/IEEE International Conference on Biomedical Computing, 2012, 14-19. (7.5% acceptance rate, Best Paper Award)
21. Lipscomb TJ, Zou A, Cho SS. Parallel Verlet neighbor list algorithm for GPU-optimized MD simulations. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2012, 321-328. (21% acceptance rate)
Highlighted by GPU Science (link)
20. Koculi E, Cho SS, Desai R, Thirumalai D, Woodson SA. Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures. Nucl. Acid Res., 2012, 40, 1-10.
19. Guthold M, Cho SS. Fibrinogen unfolding mechanisms are not too much of a stretch. Structure, 2011, 19, 1536-1538.
18. Biyun S, Cho SS, Thirumalai D. Folding of human telomerase RNA pseudoknot using ion-jump and temperature quench simulations. J. Amer. Chem. Soc. 2011, 133, 20634–20643.
Highlighted by J. Amer. Chem. Soc. (link)
17. Cho SS, Reddy G, Straub JE, Thirumalai D. Molecular mechanism for the entropic stabilization of proteins by TMAO. J. Phys. Chem. B 2011, 115, 13401-13407.
16. Patro R, Ip CY, Bista S, Cho SS, Thirumalai D, Varshney A. MDMap : A system for data-driven layout and exploration of molecular dynamics simulations. IEEE Symposium on Biological Data Visualization, 2011, 111-118.
15. Cho SS, Pincus DL, Thirumalai D. Assembly mechanisms of RNA pseudoknots are determined by the stabilities of the constituent secondary structures. Proc. Natl. Acad. Sci., USA. 2009, 106 (41):17349-17354.
14. Cho SS, Levy Y, Wolynes PG. Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics. Proc. Natl. Acad. Sci., USA. 2009, 106 (2):434-439.
13. Lenz P, Cho SS, Wolynes PG. Analysis of single molecule folding studies with replica correlation functions. Chem. Phys. Lett. 2009, 471 (4-6):310-314.
12. Pincus DL, Cho SS, Hyeon C, Thirumalai D, Minimal models for protein and RNA: From folding to function, Chapter 6 in Progress in Molecular Biology and Translational Science edited by P. Michael Conn, 2008, Academic Press, Vol. 84.
11. Cho SS, Weinkam P, Wolynes PG. Origins of barriers and barrierless folding of BBL. Proc. Natl. Acad. Sci., USA. 2008, 105 (1):118-123.
10. Ferreiro DU, Cervantes CF, Truhlar SME, Cho SS, Wolynes PG, Komives EA. Stabilizing IkBa by 'consensus' design. J. Mol. Biol. 2007, 365 (4): 1201-1216.
9. Cho SS, Levy Y, Wolynes PG. P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes. Proc. Natl. Acad. Sci., USA. 2006, 103 (3): 586-591.
8. Ferreiro DU, Cho SS, Komives EA, Wolynes PG. The energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family. J. Mol. Biol. 2005, 354 (4): 679-692.

7. Cho SS, Levy Y, Onuchic JN, Wolynes PG. Overcoming residual frustration in domain-swapping: The roles of disulfide bonds in dimerization and aggregation. Phys. Biol. 2005, 2: S44-S55.

6. Levy Y, Cho SS, Shen T, Onuchic JN, Wolynes PG. Symmetry and frustration in protein energy landscapes: A near degeneracy resolves the Rop dimer-folding mystery. Proc. Natl. Acad. Sci., USA. 2005, 102 (7):2373-2378.
5. Levy Y, Cho SS, Onuchic JN, Wolynes PG. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J. Mol. Biol. 2005, 346 (4): 1121-1145.
4. Yang SC, Cho SS, Levy Y, Cheung MS, Levine H, Wolynes PG, Onuchic JN. Domain swapping is a consequence of minimal frustration. Proc. Natl. Acad. Sci., USA. 2004, 101 (38): 13786-13791.
3. Wymore T, Hempel J, Cho SS, MacKerell AD, Nicholas HB, Deerfield DW. Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation. Proteins 2004, 57 (4): 758-771.
2. Pan YP, Huang N, Cho SS, MacKerell AD. Consideration of molecular weight during compound selection in virtual target-based database screening. J. Chem. Inf. Comp. Sci. 2003, 43 (1): 267-272.
1. Izaguirre G, Pietruszko R, Cho SS, MacKerell AD. Human aldehyde dehydrogenase catalytic activity and structural interactions with coenzyme analogs. J. Biomol. Struct. Dyn. 2001, 19(3):429-447.