Shi-Jie Chen

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 41

Top Topics

Molecular Dynamics Simulations

Hepatitis C Virus

Single Molecule

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

The journal of physical chemistry. B

Nucleic acids research

Journal of chemical theory and computation

This page only lists publications with an associated author ORCID identifier.

Publications

Yuanzhe Zhou, Shi-Jie Chen
Advances in machine-learning approaches to RNA-targeted drug design. Artificial intelligence chemistry 2 (1) (2024)
Yuanzhe Zhou, Shi-Jie Chen
Advances in machine-learning approaches to RNA-targeted drug design. Artificial intelligence chemistry 2 (1) (2024)
Yelixza I Avila, Laura P Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M J Lilley, Robin E Stanley, Ya-Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi-Jie Chen, Nikolay V Dokholyan, Cheemeng Tan, S Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W Binzel, Peixuan Guo, Kirill A Afonin
Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology. ACS applied bio materials 7 (6) (2024)
Yelixza I Avila, Laura P Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M J Lilley, Robin E Stanley, Ya-Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi-Jie Chen, Nikolay V Dokholyan, Cheemeng Tan, S Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W Binzel, Peixuan Guo, Kirill A Afonin
Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology. ACS applied bio materials (2024)
Lei Jin, Sicheng Zhang, Zhenwei Song, Xiao Heng, Shi-Jie Chen
Kinetic pathway of HIV-1 TAR cotranscriptional folding. Nucleic acids research (2024)
Yelixza I Avila, Laura P Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M J Lilley, Robin E Stanley, Ya-Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi-Jie Chen, Nikolay V Dokholyan, Cheemeng Tan, S Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W Binzel, Peixuan Guo, Kirill A Afonin
Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology. ACS applied bio materials 7 (6) (2024)
Lei Jin, Sicheng Zhang, Zhenwei Song, Xiao Heng, Shi-Jie Chen
Kinetic pathway of HIV-1 TAR cotranscriptional folding. Nucleic acids research 52 (10) (2024)
Lei Jin, Sicheng Zhang, Zhenwei Song, Xiao Heng, Shi-Jie Chen
Kinetic pathway of HIV-1 TAR cotranscriptional folding. Nucleic acids research 52 (10) (2024)
Yelixza I Avila, Laura P Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M J Lilley, Robin E Stanley, Ya-Ming Hou, Haoyun Yang, Joanna Sztuba-Solinska, Shi-Jie Chen, Nikolay V Dokholyan, Cheemeng Tan, S Kevin Li, Xiaoming He, Xiaoting Zhang, Wayne Miles, Elisa Franco, Daniel W Binzel, Peixuan Guo, Kirill A Afonin
Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology. ACS applied bio materials 7 (6) (2024)
Yuanzhe Zhou, Shi-Jie Chen
Advances in machine-learning approaches to RNA-targeted drug design. Artificial intelligence chemistry 2 (1) (2024)
Yuanzhe Zhou, Yangwei Jiang, Shi-Jie Chen
SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening. Journal of chemical theory and computation (2024)
Lei Jin, Sicheng Zhang, Zhenwei Song, Xiao Heng, Shi-Jie Chen
Kinetic pathway of HIV-1 TAR cotranscriptional folding. Nucleic acids research 52 (10) (2024)
Lei Jin, Sicheng Zhang, Zhenwei Song, Xiao Heng, Shi-Jie Chen
Kinetic pathway of HIV-1 TAR cotranscriptional folding. Nucleic acids research 52 (10) (2024)
Jun Li, Shi-Jie Chen
RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling. Nucleic acids research (2023)
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Yuanzhe Zhou, Shi-Jie Chen
Graph deep learning locates magnesium ions in RNA. QRB discovery 3 (2022)
Jun Li, Sicheng Zhang, Dong Zhang, Shi-Jie Chen
Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences. Bioinformatics (Oxford, England) 38 (16) (2022)
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Xiaojun Xu, Lei Jin, Liangxu Xie, Shi-Jie Chen
Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding. Journal of chemical theory and computation 18 (3) (2022)
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-Ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America 120 (1) (2022)
Travis Hurst, Shi-Jie Chen
Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias. The journal of physical chemistry. B 125 (4) (2021)
Yuanzhe Zhou, Yangwei Jiang, Shi-Jie Chen
RNA-ligand molecular docking: advances and challenges. Wiley interdisciplinary reviews. Computational molecular science 12 (3) (2021)
Dong Zhang, Shi-Jie Chen, Ruhong Zhou
Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. The journal of physical chemistry. B 125 (43) (2021)
Zhenwei Song, Thomas Gremminger, Gatikrushna Singh, Yi Cheng, Jun Li, Liming Qiu, Juan Ji, Margaret J Lange, Xiaobing Zuo, Shi-Jie Chen, Xiaoqin Zou, Kathleen Boris-Lawrie, Xiao Heng
The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic acids research 49 (10) (2021)
Dong Zhang, Jun Li, Shi-Jie Chen
IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures. Journal of chemical theory and computation 17 (3) (2021)
Yi Cheng, Sicheng Zhang, Xiaojun Xu, Shi-Jie Chen
Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. The journal of physical chemistry. B 125 (36) (2021)
Li-Zhen Sun, Yangwei Jiang, Yuanzhe Zhou, Shi-Jie Chen
RLDOCK: A New Method for Predicting RNA-Ligand Interactions. Journal of chemical theory and computation 16 (11) (2020)
Dong Zhang, Travis Hurst, Dongsheng Duan, Shi-Jie Chen
Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. Proceedings of the National Academy of Sciences of the United States of America 116 (18) (2019)
Shi-Jie Chen
Minimizing off-target effects in CRISPR-Cas9 genome editing. Cell biology and toxicology 35 (5) (2019)
Dong Zhang, Shi-Jie Chen
IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding. Journal of chemical theory and computation 14 (4) (2018)
Xiaojun Xu, Shi-Jie Chen
Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates. The journal of physical chemistry. B 122 (21) (2018)
Travis Hurst, Xiaojun Xu, Peinan Zhao, Shi-Jie Chen
Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. The journal of physical chemistry. B 122 (18) (2018)
Ting-Ting Sun, Chenhan Zhao, Shi-Jie Chen
Predicting Cotranscriptional Folding Kinetics For Riboswitch. The journal of physical chemistry. B 122 (30) (2018)
Li-Zhen Sun, Clayton Kranawetter, Xiao Heng, Shi-Jie Chen
Predicting Ion Effects in an RNA Conformational Equilibrium. The journal of physical chemistry. B 121 (34) (2017)
Zhichiao Miao, Ryszard W Adamiak, Maciej Antczak, Robert T Batey, Alexander J Becka, Marcin Biesiada, Michał J Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Fang-Chieh Chou, Adrian R Ferré-D'Amaré, Rhiju Das, Wayne K Dawson, Feng Ding, Nikolay V Dokholyan, Stanisław Dunin-Horkawicz, Caleb Geniesse, Kalli Kappel, Wipapat Kladwang, Andrey Krokhotin, Grzegorz E Łach, François Major, Thomas H Mann, Marcin Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw J Patel, Joseph A Piccirilli, Mariusz Popenda, Katarzyna J Purzycka, Aiming Ren, Greggory M Rice, John Santalucia, Joanna Sarzyńska, Marta Szachniuk, Arpit Tandon, Jeremiah J Trausch, Siqi Tian, Jian Wang, Kevin M Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Zok, Eric Westhof
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA (New York, N.Y.) 23 (5) (2017)
Clayton Kranawetter, Samantha Brady, Lizhen Sun, Mark Schroeder, Shi-Jie Chen, Xiao Heng
Nuclear Magnetic Resonance Study of RNA Structures at the 3'-End of the Hepatitis C Virus Genome. Biochemistry 56 (37) (2017)