Yunjie Zhao

发表

Automated and fast building of three-dimensional RNA structures

Yangyu Huang, Yunjie Zhao, Zhou Gong, 2012, Scientific Reports.

A Network of Conformational Transitions in the Apo Form of NDM-1 Enzyme Revealed by MD Simulation and a Markov State Model.

Yunjie Zhao, Yunjie Zhao, Kaifu Gao, 2017, The journal of physical chemistry. B.

RNA Stability Under Different Combinations of Amber Force Fields and Solvation Models

Yi Xiao, Yunjie Zhao, Zhou Gong, 2010, Journal of biomolecular structure & dynamics.

Propagation characteristics of weak signal in feedforward Izhikevich neural networks

Yunjie Zhao, Ya Jia, Lulu Lu, 2020 .

Effect of external periodic signals and electromagnetic radiation on autaptic regulation of neuronal firing.

Ya Jia, Xuan Zhan, Lijian Yang, 2018, IET systems biology.

3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

Jian Wang, Yunjie Zhao, Yi Xiao, 2015, Nucleic acids research.

3 dRNAscore : a distance and torsion angle dependent evaluation function of 3 D RNA structures

Jian Wang, Yi Xiao, Yunjie Zhao, 2015 .

Direct Information Reweighted by Contact Templates: Improved RNA Contact Prediction by Combining Structural Features

Yunjie Zhao, Chen Zeng, Yiren Jian, 2017, 1711.10674.

Design of Tat-Activated Cdk9 Inhibitor

F. Kashanchi, Yunjie Zhao, Chenghang Du, 2018, International Journal of Peptide Research and Therapeutics.

Novel method to identify group-specific non-catalytic pockets of human kinome for drug design

Ya Jia, Yunjie Zhao, Huiwen Wang, 2020, RSC advances.

A computational study of Tat-CDK9-Cyclin binding dynamics and its implication in transcription-dependent HIV latency.

Ya Jia, Yunjie Zhao, Huiwen Wang, 2020, Physical chemistry chemical physics : PCCP.

Computational study of non-catalytic T-loop pocket on CDK proteins for drug development

F. Kashanchi, Yunjie Zhao, Huiwen Wang, 2017 .

Insights into Temperature and Hypoxia Tolerance in Cowpea Weevil via HIF-1

Yunjie Zhao, Z. Gao, Qin Liu, 2021, Pathogens.

Twisting mode of supercoil leucine-rich domain mediates peptide sensing in FLS2–flg22–BAK1 complex

Yunjie Zhao, Chen Zeng, Peng Ran, 2020 .

Prediction of allosteric druggable pockets of cyclin-dependent kinases

Yunjie Zhao, Huiwen Wang, Chen Zeng, 2022, Briefings Bioinform..

RPpocket: An RNA–Protein Intuitive Database with RNA Pocket Topology Resources

Yunjie Zhao, Rui Yang, Haoquan Liu, 2022, International journal of molecular sciences.

Computational study of switching mechanism in add A-riboswitch

Yunjie Zhao, Huiwen Wang, Linlu Song, 2020 .

Computational study of stability of an H-H-type pseudoknot motif.

Jian Wang, Yi Xiao, Yunjie Zhao, 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

Propagation characteristics of weak signal in feedforward Izhikevich neural networks

Yunjie Zhao, Mengyan Ge, Ying Xu, 2019, Nonlinear Dynamics.

Performance of protein-ligand docking with CDK4/6 inhibitors: a case study.

Yunjie Zhao, J. Hou, Linlu Song, 2020, Mathematical biosciences and engineering : MBE.

Computational Study of Unfolding and Regulation Mechanism of preQ1 Riboswitches

Yunjie Zhao, Yi Xiao, Changjun Chen, 2012, PloS one.

Tcf1 and Lef1 transcription factors establish CD8+ T cell identity through intrinsic HDAC activity

Chen Zeng, Yunjie Zhao, Qiang Shan, 2016, Nature Immunology.

Intrinsic fluctuation and susceptibility in somatic cell reprogramming process

Qiliang Li, Yunjie Zhao, Xinyu Wang, 2019, Chinese Physics B.

Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure

Yunjie Zhao, Yi Xiao, Yi Xiao, 2011, Journal of biomolecular structure & dynamics.

Methods and applications of RNA contact prediction

Yunjie Zhao, Huiwen Wang, Yunjie Zhao, 2020, Chinese Physics B.

Evaluating native-like structures of RNA-protein complexes through the deep learning method

Soroush Vosoughi, Yunjie Zhao, Chen Zeng, 2023, Nature Communications.

Methods and Applications in Proteins and RNAs

Yunjie Zhao, Zhou Gong, Haoquan Liu, 2023, Life.

Molecular Dynamics Simulation Reveals Insights into the Mechanism of Unfolding by the A130T/V Mutations within the MID1 Zinc-Binding Bbox1 Domain

Chen Zeng, Yunjie Zhao, M. Massiah, 2015, PloS one.

RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

Yunjie Zhao, Huiwen Wang, Chen Zeng, 2021, BMC Bioinform..

Effects of Lycium barbarum Polysaccharides on Health and Aging of C. elegans Depend on daf-12/daf-16

Xuan Zhan, Lijian Yang, Yunjie Zhao, 2019, Oxidative medicine and cellular longevity.

HOW FAR AND HOW FAST CAN ONE MOVE ON NEUTRAL NETWORK

Chenghang Du, Hao Chen, Yunjie Zhao, 2013 .

HKPocket: human kinase pocket database for drug design

Ya Jia, Ying Xu, Huiwen Wang, 2019, BMC Bioinformatics.

Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations

Yunjie Zhao, Yi Xiao, Yong Duan, 2014, PloS one.

Role of Ligand Binding in Structural Organization of Add A-riboswitch Aptamer: A Molecular Dynamics Simulation

Yunjie Zhao, Yi Xiao, Changjun Chen, 2011, Journal of biomolecular structure & dynamics.

Trace, Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry: A Case Study from Single-Cell Metabolomics.

Yunjie Zhao, Chen Zeng, P. Nemes, 2019, Analytical chemistry.

Wave propagation and synchronization induced by chemical autapse in chain Hindmarsh-Rose neural network

Huiwen Wang, Yunjie Zhao, Ying Xu, 2019, Appl. Math. Comput..

Spiking activities in chain neural network driven by channel noise with field coupling

Ying Liu, Yunjie Zhao, Ping Wang, 2019, Nonlinear Dynamics.

Network Analysis Reveals the Recognition Mechanism for Dimer Formation of Bulb-type Lectins

H. H. Huang, Yunjie Zhao, Chen Zeng, 2017, Scientific Reports.

DIRECT: RNA contact predictions by integrating structural patterns

Chen Zeng, Zhichao Liu, Huiwen Wang, 2019, BMC Bioinformatics.

RBind: computational network method to predict RNA binding sites

Chen Zeng, Huiwen Wang, Yunjie Zhao, 2018, Bioinform..

Break CDK2/Cyclin E1 Interface Allosterically with Small Peptides

Chen Zeng, Yunjie Zhao, Yanzhao Huang, 2014, PloS one.

A new role for STAT3 as a regulator of chromatin topology

Yunjie Zhao, Anatoly Dritschilo, Yunjie Zhao, 2013, Transcription.

Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis

Jian Wang, Chen Zeng, Yi Zhang, 2017, Nucleic acids research.

Evaluation of RNA secondary structure prediction for both base-pairing and topology

Yi Xiao, Chen Zeng, Jun Wang, 2018, Biophysics Reports.

The TAR binding dynamics and its implication in Tat degradation mechanism.

Yunjie Zhao, Chen Zeng, Shangbo Ning, 2021, Biophysical journal.

Large-scale study of long non-coding RNA functions based on structure and expression features

Yi Zhao, Haitao Luo, Jian Wang, 2013, Science China Life Sciences.

Design of Tat-Activated Cdk9 Inhibitor

F. Kashanchi, Yunjie Zhao, Chenghang Du, 2018, International Journal of Peptide Research and Therapeutics.

Study on propagation efficiency and fidelity of subthreshold signal in feed-forward hybrid neural network under electromagnetic radiation

Yunjie Zhao, Ya Jia, Lulu Lu, 2021, Nonlinear Dynamics.

Knowledge from Large-Scale Protein Contact Prediction Models Can Be Transferred to the Data-Scarce RNA Contact Prediction Task

Soroush Vosoughi, Yunjie Zhao, Chen Zeng, 2023, ArXiv.

DIRECT: RNA contact predictions by integrating structural patterns

Yunjie Zhao, Huiwen Wang, Chen Zeng, 2019, BMC Bioinformatics.

RBinds: A user-friendly server for RNA binding site prediction

Yunjie Zhao, Huiwen Wang, Yunjie Zhao, 2020, Computational and structural biotechnology journal.

HKPocket: human kinase pocket database for drug design

Yunjie Zhao, Ying Xu, Huiwen Wang, 2019, BMC Bioinformatics.

RPflex: A Coarse-Grained Network Model for RNA Pocket Flexibility Study

Yunjie Zhao, Chen Zeng, Haoquan Liu, 2023, International journal of molecular sciences.

DLSSAffinity: protein-ligand binding affinity prediction via a deep learning model.

Yunjie Zhao, Huiwen Wang, Chen Zeng, 2022, Physical chemistry chemical physics : PCCP.

Automated building of three-dimensional RNA structures

Yi Xiao, Yangyu Huang, Chen Zeng, 2013 .