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Plos One|March 24, 2015
TBI server: a web server for predicting ion effects in RNA foldingYuhong Zhu, Zhaojian He, Shi-Jie ChenWiley Interdisciplinary Reviews. Computational Molecular Science|June 9, 2023
RNA-ligand molecular docking: advances and challengesYuanzhe Zhou, Yangwei Jiang, Shi-Jie ChenThe Journal of Physical Chemistry. B|October 25, 2021
Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 ModelDong Zhang, Shi-Jie Chen, Ruhong ZhouMethods in Molecular Biology (Clifton, N.J.)|October 8, 2017
Predicting RNA Structure with VfoldChenhan Zhao, Xiaojun Xu, Shi-Jie ChenRNA (New York, N.Y.)|April 23, 2014
Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairingSong Cao, Xiaojun Xu, Shi-Jie ChenPlos One|September 13, 2014
Vfold: a web server for RNA structure and folding thermodynamics predictionXiaojun Xu, Peinan Zhao, Shi-Jie ChenScientific Reports|March 10, 2017
CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessmentXiaojun Xu, Dongsheng Duan, Shi-Jie ChenJournal of Structural Biology|June 8, 2019
VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structuresXiaojun Xu, Chenhan Zhao, Shi-Jie ChenJournal of Chemical Theory and Computation|August 16, 2024
SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual ScreeningYuanzhe Zhou, Yangwei Jiang, Shi-Jie ChenCurrent Opinion in Structural Biology|May 30, 2024
Embracing exascale computing in nucleic acid simulationsJun Li, Yuanzhe Zhou, Shi-Jie ChenPageof 18