Publications
Google Scholar | ORCiD | Publons | Scopus | ResearchGate | PubMed
† Equal contribution * Corresponding author
48. Young-Moo Byun & Jejoong Yoo*
GPU acceleration of many-body pertur- bation theory methods in MOLGW with OpenACC
47. Jong-Hyun Won†, Jae-Won Lee†, Seonggwang Jeon†, Yujin Choo†, Yubin Yeon†, Jin-Seon Oh†, Minsoo Kim†, SeonHwa Kim, InSuk Joung, Cheongjae Jang, Sung Jong Lee, Tae Hyun Kim, Kyong Hwan Jin, Giltae Song, Eun-Sol Kim, Jejoong Yoo, Eunok Paek, Yung-Kyun Noh* & Keehyoung Joo*
Deepfold: Enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
46. Ki-Baek Jeong, Minju Ryu, Jin-Sik Kim, Minsoo Kim, Jejoong Yoo, Minji Chung, Sohee Oh, Gyunghee Jo, Seong-Gyu Lee, Ho Min Kim, Mi-Kyung Lee* & Seung- Wook Chi*
Single-molecule fingerprinting of protein-drug interaction using a funneled biological nanopore
45. Seu-Na Lee, Hwa-Jin Cho, Hyeongseop Jeong, Bumhan Ryu, Hyuk-Joon Lee, Minsoo Kim, Jejoong Yoo, Jae-Sung Woo* & Hyung Ho Lee*
Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel
44. Hyuk-Joon Lee, Hyung Jin Cha, Hyeongseop Jeong, Seu-Na Lee, Chang-Won Lee, Minsoo Kim, Jejoong Yoo, Jae-Sung Woo*
Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM
43. Minchae Kang, Minsoo Kim, Min Wook Kim, Yewon Shin, Jejoong Yoo* & Sang Hak Lee*
Aggregation or phase separation can be induced in highly charged proteins by small charged biomolecules
42. Minjung Kim, Sehui Bae, Inrok Oh, Jejoong Yoo & Jun Soo Kim*
Sequence-dependent twist-bend coupling in DNA minicircles
41. Jejoong Yoo*, Sangwoo Park, Christopher Maffeo, Taekjip Ha* & Aleksei Aksimentiev*
DNA Sequence and Methylation Prescribe the Inside-Out Conforma- tional Dynamics and Bending Energetics of DNA Minicircles
40.Sehui Bae, Inrok Oh, Jejoong Yoo & Jun Soo Kim*
Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA
39. Jejoong Yoo*
On the stability of protein–DNA complexes in molecular dynamics simulations using the CUFIX corrections
38. Hyuk-Joon Lee†, Hyeongseop Jeong†, Jaekyung Hyun†, Bumhan Ryu, Kunwoong Park, Hyun-Ho Lim, Jejoong Yoo & Jae-Sung Woo*
Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel
37. Jejoong Yoo*, David Winogradoff & Aleksei Aksimentiev*
Molecular Dynamics Simulations of DNA-DNA and DNA-Protein Interactions
36. Seonju You, Hong-guen Lee, Kimoon Kim & Jejoong Yoo*
Improved Parameterization of Protein–DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA
Journal of Chemical Theory and Computation, 16:4006–4013, 2020
35. Wooseup Hwang, Jejoong Yoo, In-Chul Hwang, Jiyeon Lee, Young Ho Ko, Hyun Woo Kim, Younghoon Kim, Yeonsang Lee, Moon Young Hur, Kyeng Min Park, Jongcheol Seo, Kangkyun Baek & Kimoon Kim
Hierarchical Self-assembly of Polypseudorotaxanes into Artificial Microtubules
34. Younghoon Kim, Jaehyoung Koo, In-Chul Hwang, Rahul Dev Mukhopadhyay, Soonsang Hong, Jejoong Yoo, Ajaz Dar, Ikjin Kim, Dohyun Moon, Tae Joo Shin, Young Ko & Kimoon Kim
Rational Design and Construction of Hierarchical Superstructures Using Shape-persistent Organic Cages: Porphyrin Box-based Metallosupramolecular Assemblies
Journal of the American Chemical Society, 140:14547–14551, 2018
33. Hyunju Kang†, Jejoong Yoo†, Hong Soo Lee, Byeong-Kwon Sohn, Seung-Won Lee, Wenjie Ma, Jung-Min Kee, Aleksei Aksimentiev* & Hajin Kim*
Sequence-dependent DNA condensation as a driving force of DNA phase separation
32. Alexander Ohmann, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N Baumann, Kerstin Gopfrich, Jejoong Yoo, Ulrich F Keyser* & Aleksei Aksimentiev*
A synthetic enzyme built from DNA flips 10^7 lipids per second in biological membranes
31. Jejoong Yoo & Aleksei Aksimentiev
New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions
Physical Chemistry Chemical Physics, 20:8432–8449, 2018 (2018 PCCP Hot Articles)
30. Kyeng Min Park, Kangkyun Baek, Young Ho Ko, Annadka Shrinidhi, James Murray, Won Hyuk Jang, Ki Hean Kim, Jun-Seok Lee, Jejoong Yoo, Sungwan Kim & Kimoon Kim
Mono-allyloxylated Cucurbit[7]uril Acts as an Unconventional Amphiphile to Form Light-responsive Vesicles
29. Jejoong Yoo & Aleksei Aksimentiev
Refined Parametrization of Non-bonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations
The Journal of Physical Chemistry Letters, 7:3812–3818, 2016
28. Kerstin Gopfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev & Ulrich F. Keyser
Large-Conductance Transmembrane Porin Made from DNA Origami
27. Kerstin Gopfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev & Ulrich F. Keyser
Ion channels made from a single membrane-spanning DNA duplex
26. Scott Michael Slone, Chen-Yu Li, Jejoong Yoo & Aleksei Aksimentiev “Molecular mechanics of DNA bricks: In situ structure, mechanical properties and ionic conductivity.” New Journal of Physics, 18:055012, 2016 [Full text]
25. Jejoong Yoo, James Wilson & Aleksei Aksimentiev
Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields
24. Swati Bhattacharya†, Jejoong Yoo† & Aleksei Aksimentiev
Water mediates recognition of DNA sequence via ionic current blockade in a biological nanopore.
23. Chris Maffeo, Jejoong Yoo & Aleksei Aksimentiev
De novo prediction of DNA origami structures through atomistic molecular dynamics simulation
22. Jejoong Yoo†, Hajin Kim†, Aleksei Aksimentiev & Taekjip Ha
Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation
21. Thuy Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei Aksimentiev & Taekjip Ha
Effect of cytosine modifications on DNA flexibility and nucleosome mechanical stability
20. Jejoong Yoo & Aleksei Aksimentiev
The structure and intermolecular forces of DNA condensates
19. Jejoong Yoo & Aleksei Aksimentiev
Improved parameterization of amine–carboxyate and amine–phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields
Journal of Chemical Theory and Computation, 12:430–443, 2016
18. Jejoong Yoo & Aleksei Aksimentiev
Molecular dynamics of membrane-spanning DNA channels: Conductance mechanism, electro-osmotic transport and mechanical gating
The Journal of Physical Chemistry Letters, 6:4680–4687, 2015
17. Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernandez-Ainsa, Ulrich F. Keyser & Aleksei Aksimentiev
Ionic conductivity, structural deformation and programmable anisotropy of DNA origami in electric field.
16. Chris Maffeo, Jejoong Yoo, Jeffrey Comer, David Wells, Binquan Luan & Aleksei Aksimentiev
Close encounters with DNA.
15. Jejoong Yoo & Aleksei Aksimentiev
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.
Proceedings of the National Academy of Sciences, 110:20099–20104, 2013.
14. Jejoong Yoo, Meyer Jackson & Qiang Cui
A comparison of coarse-grained and continuum models for membrane bending in lipid bilayer fusion pores.
13. Jejoong Yoo & Qiang Cui
Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-grained simulation analysis of gramicidin A association.
12. Jejoong Yoo & Qiang Cui
Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A.
11. Chris Maffeo, Swati Bhattacharya, Jejoong Yoo, David Wells & Aleksei Aksimentiev
Modeling and simulation of ion channels.
10. Jejoong Yoo & Aleksei Aksimentiev
Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations.
9. Jejoong Yoo & Aleksei Aksimentiev
Improved parametrization of Li+, Na+, K+, and Mg2+ ions for all-atom molecular dynamics simulations of nucleic acid systems.
8. Jejoong Yoo & Qiang Cui
Chemical versus mechanical perturbations on the protonation state of arginine in complex lipid membranes: insights from microscopic pKa calculations.
7. Jejoong Yoo & Qiang Cui
Curvature generation and pressure profile modulation in membrane by lysolipids: Insights from Coarse-Grained Simulations.
6. Yuye Tang, Xi Chen, Jejoong Yoo, Arun Yethiraj & Qiang Cui
Numerical simulation of nanoindentation and patch clamp experiments on mechanosensitive channels of large conductance in escherichia coli.
5. Jejoong Yoo & Qiang Cui
Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations.
4. Xi Chen, Qiang Cui, Yuye Tang, Jejoong Yoo & Arun Yethiraj
Gating mechanisms of mechanosensitive channels of large conductance, I: a continuum mechanics-based hierarchical framework.
3. Yuye Tang, Jejoong Yoo, Arun Yethiraj, Qiang Cui & Xi Chen
Gating mechanisms of mechanosensitive channels of large conductance, II: systematic study of conformational transitions.
2. Yuye Tang, Jejoong Yoo, Arun Yethiraj, Qiang Cui & Xi Chen
Mechanosensitive channels: insights from continuum-based simulations.
1. Yuye Tang, Guoxin Cao, Xi Chen, Jejoong Yoo, Arun Yethiraj & Qiang Cui
A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL.
† Equal contribution
* Corresponding author