肖奕｜华中科技大学｜学者主页

2026

3dDNAi: An Integrated Approach for 3D Structure Prediction of Single-Stranded DNAs

Yi Zhang, Yiduo Xiong, Yi Xiao

Journal of Chemical Theory and Computation

DOI

2025

Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations

Peng Tao, Yunda Si, Jie Xia, Yi Xiao

PLoS Computational Biology

DOI

2025

Pathway regulation mechanism by cotranslational protein folding

Peng Tao, Yi Xiao

Communications Chemistry

DOI

2025

Charge Arrangement Determines the Sensitivity of Aggregation Patterns between Peptide-Chains to the Surrounding Ionic Environment

Lei Bao, Wen-Bin Kang, Ben‐Chao Zhu, Yi Xiao

Journal of Chemical Information and Modeling

DOI

2024

3dRNA/DNA: 3D Structure Prediction from RNA to DNA

Yi Zhang, Yiduo Xiong, Chenxi Yang, Yi Xiao

Journal of Molecular Biology

DOI

2024

3dDNAscoreA: A scoring function for evaluation of DNA 3D structures

Yi Zhang, Chenxi Yang, Yiduo Xiong, Yi Xiao

Biophysical Journal

DOI

2024

RNA-Puzzles Round V: blind predictions of 23 RNA structures

Fan Bu, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa R. H. de Aquino, Nagendar Goud Badepally, Robert Batey, Eugene F. Baulin, Paweł Boiński, Michal J. Boniecki, Janusz Marek Bujnicki, Kristy A. Carpenter, Jose Chacon, Shi‐Jie Chen, Wah Keung Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne Dawson, Frank DiMaio, Feng Ding, Anne‐Catherine Dock‐Brégeon, Nikolay V. Dokholyan, Ron O. Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian R. Ferré-D’Amaré, Caleb Geniesse, George E. Ghanim, Horacio V. Guzman, Iris V. Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S. Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael C. Kretsch, Mateusz Kurciński, Jun Li, Shuang Li, Marcin Magnus, Benoı̂t Masquida, Seyed Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory I. Nikolaev, Chandran Nithin, Grace Nye, Iswarya P. N. Pandaranadar Jeyeram, Alberto Pérez, Phillip H. Pham, Joseph A. Piccirilli, Smita P. Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Łukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzyńska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna Chaitanya Suddala, Marta Szachniuk, Raphael J.L. Townshend, Robert J. Trachman, Jian Wang, Wenkai Wang, Andrew M. Watkins, Tomasz K. Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Żok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Éric Westhof, Zhichao Miao

Nature Methods

DOI

2024

All-atom RNA structure determination from cryo-EM maps

Tao Li, Jiahua He, Hong Cao, Yi Zhang, Ji Chen, Yi Xiao, Sheng‐You Huang

Nature Biotechnology

DOI

2023

Using 3dRNA/DNA for RNA and DNA 3D Structure Prediction and Evaluation

Yiduo Xiong, Yi Zhang, Jian Wang, Yi Xiao

Current Protocols

DOI

2023

Data-driven detection of critical points of phase transitions in complex systems

Peng Tao, Chenghang Du, Yi Xiao, Chen Zeng

Communications Physics

DOI

2022

3dRNA: 3D Structure Prediction from Linear to Circular RNAs

Yi Zhang, Jun Wang, Yi Xiao

Journal of Molecular Biology

DOI

2022

HDOCK update for modeling protein‐ RNA / DNA complex structures

Hao Li, Eddie Huang, Yi Zhang, Sheng‐You Huang, Yi Xiao

Protein Science

DOI

2022

3dDNA: A Computational Method of Building DNA 3D Structures

Yi Zhang, Yiduo Xiong, Yi Xiao

Molecules

DOI

2022

Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction

Kangkun Mao, Jun Wang, Yi Xiao

Molecules

DOI

2022

Advances in RNA 3D Structure Prediction

Xiujuan Ou, Yi Zhang, Yiduo Xiong, Yi Xiao

Journal of Chemical Information and Modeling

DOI

2021

Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search

Kangkun Mao, Yi Xiao

Molecules

DOI

2020

Improving RNA secondary structure prediction using direct coupling analysis

Xiaoling He, Jun Wang, Jian Wang, Yi Xiao

Chinese Physics B

DOI

2020

Electrostatics of Prokaryotic Ribosome and Its Biological Implication

Jun Wang, Chitra B. Karki, Yi Xiao, Lin Li

Biophysical Journal

DOI

2020

Prediction of RNA secondary structure with pseudoknots using coupled deep neural networks

Kangkun Mao, Jun Wang, Yi Xiao

Biophysics Reports

DOI

2020

Using the generalized Born surface area model to fold proteins yields more effective sampling while qualitatively preserving the folding landscape

Peng Tao, Yi Xiao

Physical review. E

DOI

2020

Pathway regulation mechanism revealed by cotranslational folding of villin headpiece subdomain HP35

Peng Tao, Ercheng Wang, Yi Xiao

Physical review. E

DOI

2020

3dRNA: Building RNA 3D structure with improved template library

Yi Zhang, Jun Wang, Yi Xiao

Computational and Structural Biotechnology Journal

DOI

2020

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Michał J. Boniecki, Janusz Marek Bujnicki, Shi‐Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang‐Chieh Chou, Rhiju Das, Nikolay V. Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, A. Krokhotin, Marcin Magnus, Olivier Mailhot, François Major, Thomas H. Mann, Paweł Piątkowski, Radosław Pluta, Mariusz Popenda, Joanna Sarzyńska, Lizhen Sun, Marta Szachniuk, Siqi Tian, Jian Wang, Jun Wang, Andrew M. Watkins, Jakub Wiedemann, Yi Xiao, Xiaojun Xu, Joseph David Yesselman, Dong Zhang, Yi Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Żok, Adriana Żyła, Aiming Ren, Robert Batey, Barbara L. Golden, Lin Huang, David M.J. Lilley, Yijin Liu, Dinshaw J. Patel, Éric Westhof

RNA

DOI

2019

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures

Jiahua He, Jun Wang, Huanyu Tao, Yi Xiao, Sheng‐You Huang

Nucleic Acids Research

DOI

2019

3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction

Jun Wang, Jian Wang, Yanzhao Huang, Yi Xiao

International Journal of Molecular Sciences

DOI

2019

Molecular dynamics simulation of the binding process of ligands to the add adenine riboswitch aptamer

Lei Bao, Jun Wang, Yi Xiao

Physical review. E

DOI

2019

A novel folding pathway of the villin headpiece subdomain HP35

Ercheng Wang, Peng Tao, Jun Wang, Yi Xiao

Physical Chemistry Chemical Physics

DOI

2019

Inference of RNA structural contacts by direct coupling analysis

Xiaoling He, Shuaimin Li, Xiujuan Ou, Jun Wang, Yi Xiao

Communications in Information and Systems

DOI

2018

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

Yunjie Zhao, Jun Wang, Chen Zeng, Yi Xiao

Biophysics Reports

DOI

2017

3dRPC: a web server for 3D RNA–protein structure prediction

Yangyu Huang, Haotian Li, Yi Xiao

Bioinformatics

DOI

2017

Structural modeling of human cardiac sodium channel pore domain

Xiaofeng Ji, Yi Xiao, Shiyong Liu

Journal of Biomolecular Structure and Dynamics

DOI

2017

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

Jian Wang, Kangkun Mao, Yunjie Zhao, Chen Zeng, Jianjin Xiang, Yi Zhang, Yi Xiao

Nucleic Acids Research

DOI

2017

Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation

Jian Wang, Yi Xiao

Current Protocols in Bioinformatics

DOI

2017

3D Structure Prediction of Noncoding RNA and Single Stranded DNA

Jian Wang, Yi Xiao

Biophysical Journal

DOI

2017

A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

Haotian Li, Yangyu Huang, Yi Xiao

PLoS ONE

DOI

2017

Multistable states in a system of coupled phase oscillators with inertia

Di Yuan, Fang Lin, Limei Wang, Danyang Liu, Junzhong Yang, Yi Xiao

Scientific Reports

DOI

2017

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Robert Batey, Alexander J. Becka, Marcin Biesiada, M. Boniecki, Janusz Marek 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, A. Krokhotin, Grzegorz 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, J.J. Trausch, Siqi Tian, Jian Wang, Kevin M. Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Żok, Éric Westhof

RNA

DOI

2016

Using 3dRPC for RNA–protein complex structure prediction

Yangyu Huang, Haotian Li, Yi Xiao

Biophysics Reports

DOI

2016

Types and concentrations of metal ions affect local structure and dynamics of RNA

Jun Wang, Yi Xiao

Physical review. E

DOI

2016

Dynamics in the Kuramoto model with a bi-harmonic coupling function

Di Yuan, H. T. Cui, Junlong Tian, Yi Xiao, Yingxin Zhang

Communications in Nonlinear Science and Numerical Simulation

DOI

2015

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

Jian Wang, Yunjie Zhao, Chunyan Zhu, Yi Xiao

Nucleic Acids Research

DOI

2015

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

Jun Wang, Yunjie Zhao, Jian Wang, Yi Xiao

Physical Review E

DOI

2015

Computational evidence that fast translation speed can increase the probability of cotranslational protein folding

Ercheng Wang, Jun Wang, Changjun Chen, Yi Xiao

Scientific Reports

DOI

2015

Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space

Changjun Chen, Yi Xiao, Yanzhao Huang

Physical Review E

DOI

2015

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Zhichao Miao, Ryszard W. Adamiak, Marc-Frédérick Blanchet, Michal Boniecki, Janusz Marek Bujnicki, Shi‐Jie Chen, Clarence Yu Cheng, Grzegorz Chojnowski, Fang‐Chieh Chou, Pablo Cordero, José Almeida Cruz, Adrian R. Ferré-D’Amaré, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Stanisław Dunin-Horkawicz, Wipapat Kladwang, A. Krokhotin, Grzegorz Łach, Marcin Magnus, François Major, Thomas H. Mann, Benoı̂t Masquida, Dorota Matelska, Mélanie Meyer, Alla Peselis, Mariusz Popenda, Katarzyna J. Purzycka, Alexander Serganov, Juliusz Stasiewicz, Marta Szachniuk, Arpit Tandon, Siqi Tian, Jian Wang, Yi Xiao, Xiaojun Xu, Jinwei Zhang, Peinan Zhao, Tomasz Żok, Éric Westhof

RNA

DOI

2014

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

Rui Zhou, Gia G. Maisuradze, David Suñol, Toni Todorovski, María Jesús Macías, Yi Xiao, Harold A. Scheraga, Cezary R. Czaplewski, Adam Liwo

Proceedings of the National Academy of Sciences

DOI

2014

A fast tomographic method for searching the minimum free energy path

Changjun Chen, Yanzhao Huang, Xuewei Jiang, Yi Xiao

The Journal of Chemical Physics

DOI

2014

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

Zhou Gong, Yunjie Zhao, Changjun Chen, Yong Duan, Yi Xiao

PLoS ONE

DOI

2013

Efficiently finding the minimum free energy path from steepest descent path

Changjun Chen, Yanzhao Huang, Xiaofeng Ji, Yi Xiao

The Journal of Chemical Physics

DOI

2013

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Rocco Moretti, Sarel Jacob Fleishman, Rudi Agius, Mieczyslaw Torchala, Paul A. Bates, Panagiotis L. Kastritis, João Rodrigues, Mikael E. Trellet, Alexandre M. J. J. Bonvin, Meng Cui, Marianne J. Rooman, Dimitri Gilis, Yves Dehouck, Iain H. Moal, Miguel Romero‐Durana, Laura Pérez‐Cano, Chiara Pallara, Brian Jiménez‐García, Juan Fernández‐Recio, Samuel Coulbourn Flores, Michael S. Pacella, Krishna Praneeth Kilambi, Jeffrey J. Gray, Petr A. Popov, Sergei Grudinin, Juan Esquivel‐Rodríguez, Daisuke Kihara, Nan Zhao, Dmitry Korkin, Xiaolei Zhu, Omar Demerdash, Julie C. Mitchell, Eiji Kanamori, Yuko Tsuchiya, Haruki Nakamura, Hasup Lee, Hahnbeom Park, Chaok Seok, Jamica Sarmiento, Shide Liang, Shunsuke Teraguchi, Daron M. Standley, Hiromitsu Shimoyama, Genki Terashi, Mayuko Takeda‐Shitaka, Mitsuo Iwadate, Hideaki Umeyama, Dmitri Beglov, David R. Hall, Dima Kozakov, Sándor Vajda, Brian G. Pierce, Howook Hwang, Thom Vreven, Zhiping Weng, Yangyu Huang, Haotian Li, Xiufeng Yang, Xiaofeng Ji, Shiyong Liu, Yi Xiao, Martin Zacharias, Sanbo Qin, Huan‐Xiang Zhou, Sheng‐You Huang, Xiaoqin Zou, Sameer S Velankar, Joël Janin, Shoshana J. Wodak, David A. Baker

Proteins Structure Function and Bioinformatics

DOI

2013

How to Use Not-Always-Reliable Binding Site Information in Protein-Protein Docking Prediction

Lin Li, Yanzhao Huang, Yi Xiao

PLoS ONE

DOI

2013

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

Yi Chen Zhao, Jian Wang, Xiaowei Chen, Haitao Luo, Yunjie Zhao, Yi Xiao, Rensheng Chen

Science China Life Sciences

DOI

2013

Binding free-energy calculation of an ion-peptide complex by constrained dynamics

Changjun Chen, Yanzhao Huang, Xuewei Jiang, Yi Xiao

Physical Review E

DOI

2013

A novel protocol for three-dimensional structure prediction of RNA-protein complexes

Yangyu Huang, Shiyong Liu, Da‐Chuan Guo, Lin Li, Yi Xiao

Scientific Reports

DOI

2013

Simulation study of the role of the ribosomal exit tunnel on protein folding

Changjun Chen, Ercheng Wang, Pengyu Liu, Yi Xiao

Physical Review E

DOI

2012

Free-energy calculations along a high-dimensional fragmented path with constrained dynamics

Changjun Chen, Yanzhao Huang, Yi Xiao

Physical Review E

DOI

2012

Preorientation of protein and RNA just before contacting

Da‐Chuan Guo, Shiyong Liu, Yangyu Huang, Yi Xiao

Journal of Biomolecular Structure and Dynamics

DOI

2012

Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath

Changjun Chen, Yanzhao Huang, Yi Xiao

Journal of Biomolecular Structure and Dynamics

DOI

2012

Effects of Mutation, Truncation, and Temperature on the Folding Kinetics of a WW Domain

Gia G. Maisuradze, Rui Zhou, Adam Liwo, Yi Xiao, Harold A. Scheraga

Journal of Molecular Biology

DOI

2012

Network approach to identify the folding transition states of peptides and proteins

Xuewei Jiang, Anhua Zhong, Changjun Chen, Yanzhao Huang, Yi Xiao

Physical Review E

DOI

2012

Automated and fast building of three-dimensional RNA structures

Yunjie Zhao, Yangyu Huang, Zhou Gong, Yanjie Wang, Jianfen Man, Yi Xiao

Scientific Reports

DOI

2011

生物大分子的自由能计算方法(英文)

陈长军，黄延昭，肖奕

《生物物理学报》

2011

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

Zhou Gong, Yunjie Zhao, Changjun Chen, Yi Xiao

Journal of Biomolecular Structure and Dynamics

DOI

2011

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

Sarel Jacob Fleishman, Timothy A. Whitehead, Eva‐Maria Strauch, Jacob E. Corn, Sanbo Qin, Huan‐Xiang Zhou, Julie C. Mitchell, Omar Demerdash, Mayuko Takeda‐Shitaka, Genki Terashi, Iain H. Moal, Xiaofan Li, Paul A. Bates, Martin Zacharias, Hahnbeom Park, Jun-su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon B, Jérôme Azé, Seren Soner, Şefik Kerem Ovalı, Pemra Özbek, Nir Ben‐Tal, Türkan Haliloǧlu, Howook Hwang, Thom Vreven, Brian G. Pierce, Zhiping Weng, Laura Pérez‐Cano, Carles Pons, Juan Fernández‐Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H. Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li, Da‐Chuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Barnett‐Itzhaki, Ora Schueler‐Furman, Yuval Inbar, Vladimir Potapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita, Camden Driggers, Robert G. Hall, Jessica L. Morgan, Victor L. Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Weiyi Zhang, Carlos Jaime Camacho, Krishna Praneeth Kilambi, Aroop Sircar, Jeffrey J. Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen J. Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel‐Rodríguez, Daisuke Kihara, P. Benjamin Stranges, Ron Jacak, Brian A. Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J. Wodak, Joël Janin, David A. Baker

Journal of Molecular Biology

DOI

2011

Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure

Yunjie Zhao, Zhou Gong, Yi Xiao

Journal of Biomolecular Structure and Dynamics

DOI

2011

ASPDock: protein-protein docking algorithm using atomic solvation parameters model

Lin Li, Da‐Chuan Guo, Yangyu Huang, Shiyong Liu, Yi Xiao

BMC Bioinformatics

DOI

2011

The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel

Hongxing Lei, Changjun Chen, Yi Xiao, Yong Duan

The Journal of Chemical Physics

DOI

2011

Free Energy Calculation Methods of Biomolecules

Yi Xiao

Acta Biophysica Sinica

2011

Multi-nucleation and vectorial folding pathways of large helix protein

Rui Zhou, Yi Jie He, Yi Xiao

Computational Biology and Chemistry

DOI

2010

Symmetric Key Structural Residues in Symmetric Proteins with Beta-Trefoil Fold

Jianhui Feng, Mingfeng Li, Yanzhao Huang, Yi Xiao

PLoS ONE

DOI

2010

Improvements of network approach for analysis of the folding free‐energy surface of peptides and proteins

Xuewei Jiang, Changjun Chen, Yi Xiao

Journal of Computational Chemistry

DOI

2009

RNA分子动力学模拟中不同AMBER分子力场与溶剂模型匹配的研究

龚洲，赵蕴杰，肖奕

《生物物理学报》

2009

United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding

Yi Jie He, Changjun Chen, Yi Xiao

Journal of Computational Biology

DOI

2009

Accurate free energy calculation along optimized paths

Changjun Chen, Yi Xiao

Journal of Computational Chemistry

DOI

2009

Folding Mechanism of Beta-Hairpin Trpzip2: Heterogeneity, Transition State and Folding Pathways

Yi Xiao, Changjun Chen, Yi Jie He

International Journal of Molecular Sciences

DOI

2009

Foldable subunits of helix protein

Yi Jie He, Rui Zhou, Yanzhao Huang, Yi Xiao

Computational Biology and Chemistry

DOI

2009

STUDY OF FOLDING BEHAVIORS OF A SIX-HELIX PROTEIN BY ab initio MOLECULAR DYNAMICS FOLDING SIMULATIONS OF UNRES

Yi Jie He, Rui Zhou, Yi Xiao

International Journal of Modern Physics C

DOI

2009

Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field

Yi Jie He, Yi Xiao, Adam Liwo, Harold A. Scheraga

Journal of Computational Chemistry

DOI

2008

Observation of multiple folding pathways of β-hairpin trpzip2 from independent continuous folding trajectories

Changjun Chen, Yi Xiao

Bioinformatics

DOI

2008

Effects of external interactions on protein sequence‐structure relations of beta‐trefoil fold

Mingfeng Li, Yanzhao Huang, Yi Xiao

Proteins Structure Function and Bioinformatics

DOI

2008

A simple method of identifying symmetric substructures of proteins

Hanlin Chen, Yanzhao Huang, Yi Xiao

Computational Biology and Chemistry

DOI

2007

Structural-symmetry-related sequence patterns of the proteins of beta-propeller family

Xiaochun Wang, Yanzhao Huang, Yi Xiao

Journal of Molecular Graphics and Modelling

DOI

2007

CHAOTIC DYNAMICS OF A FIVE-DIMENSIONAL NONLINEAR NETWORK

Xuewei Jiang, DI YUAN, Yi Xiao

International Journal of Modern Physics C

DOI

2007

Hidden symmetries in the primary sequences of beta-barrel family

Xiaofeng Ji, Hanlin Chen, Yi Xiao

Computational Biology and Chemistry

DOI

2006

All‐atom contact potential approach to protein thermostability analysis

Changjun Chen, Lin Li, Yi Xiao

Biopolymers

DOI

2006

Molecular dynamics simulations of folding processes of a β-hairpin in an implicit solvent

Changjun Chen, Yi Xiao

Physical Biology

DOI

2006

Identification of key residues in proteins by using their physical characters

Changjun Chen, Lin Li, Yi Xiao

Physical Review E

DOI

2005

A Directed Essential Dynamics Simulation of Peptide Folding

Changjun Chen, Yi Xiao, Linsen Zhang

Biophysical Journal

DOI

2005

COMPOSITIONAL AND ENVIRONMENTAL DEPENDENCE OF THE STABILITY OF α-HELICES

Changjun Chen, Jianhui Feng, Linsen Zhang, Yi Xiao

International Journal of Modern Physics C

DOI

2005

LENGTH SCALE EFFECTS OF SMALL MODEL PROTEIN FOLDING

Linsen Zhang, MING ZHANG, Changjun Chen, Yi Xiao

International Journal of Modern Physics C

DOI

2005

A common sequence-associated physicochemical feature for proteins of beta-trefoil family

Ruizhen Xu, Yi Xiao

Computational Biology and Chemistry

DOI

2005

Improvement on a simplified model for protein folding simulation

Ming Zhang, Changjun Chen, Yi Jie He, Yi Xiao

Physical Review E

DOI

2005

A symmetry-related sequence-structure relation of proteins

Ruizhen Xu, Mingfen Li, Hanlin Chen, Yanzhao Huang, Yi Xiao

Chinese Science Bulletin

DOI

2004

DYNAMIC MOVES IN LATTICE SIMULATION OF PROTEIN FOLDING

Linsen Zhang, Changjun Chen, Yi Jie He, Yi Xiao

International Journal of Modern Physics C

DOI

2004

LATTICE SIMULATION OF NASCENT PEPTIDE FOLDING

JIAFENG ZHUO, Linsen Zhang, Changjun Chen, Yi Jie He, Yi Xiao

International Journal of Modern Physics B

DOI

2000

不同结构类蛋白质序列中的关联特性

黄敏，沈晖，肖奕

《生物物理学报》

1994

DNA与分形

肖奕

《物理》

1994

Comment on ‘‘Fractal study of tertiary structure of proteins’’

Yi Xiao

Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics

DOI

1994

A modified method of determining fractal dimensions of polymers and biopolymers

Yi Xiao, K.L. Yao

Acta Physica Sinica (Overseas Edition)

DOI

1986

蛋白质能带结构的晶体轨道法研究 Ⅲ金属离子和水对蛋白质能带结构的影响

肖奕，陈润生，倪向善

《生物物理学报》

1986

半经验CNDO/2晶体轨道法的程序设计及算例

肖奕，陈润生

《生物化学与生物物理进展》

1986

氨基酸残基无序排列对蛋白质分子电子能谱的影响

肖奕

《生物物理学报》

1985

蛋白质能带结构的晶体轨道法研究——Ⅱ蛋白质构象的变化对其能带结构的影响

肖奕，陈润生，石秀凡

《生物物理学报》

精选作品

期刊论文

3dDNAi: An Integrated Approach for 3D Structure Prediction of Single-Stranded DNAs

Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations

Pathway regulation mechanism by cotranslational protein folding

Charge Arrangement Determines the Sensitivity of Aggregation Patterns between Peptide-Chains to the Surrounding Ionic Environment

3dRNA/DNA: 3D Structure Prediction from RNA to DNA

3dDNAscoreA: A scoring function for evaluation of DNA 3D structures

RNA-Puzzles Round V: blind predictions of 23 RNA structures

All-atom RNA structure determination from cryo-EM maps

Using 3dRNA/DNA for RNA and DNA 3D Structure Prediction and Evaluation

Data-driven detection of critical points of phase transitions in complex systems

3dRNA: 3D Structure Prediction from Linear to Circular RNAs

HDOCK update for modeling protein‐ RNA / DNA complex structures

3dDNA: A Computational Method of Building DNA 3D Structures

Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction

Advances in RNA 3D Structure Prediction

Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search

Improving RNA secondary structure prediction using direct coupling analysis

Electrostatics of Prokaryotic Ribosome and Its Biological Implication

Prediction of RNA secondary structure with pseudoknots using coupled deep neural networks

Using the generalized Born surface area model to fold proteins yields more effective sampling while qualitatively preserving the folding landscape

Pathway regulation mechanism revealed by cotranslational folding of villin headpiece subdomain HP35

3dRNA: Building RNA 3D structure with improved template library

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures

3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction

Molecular dynamics simulation of the binding process of ligands to the add adenine riboswitch aptamer

A novel folding pathway of the villin headpiece subdomain HP35

Inference of RNA structural contacts by direct coupling analysis

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

3dRPC: a web server for 3D RNA–protein structure prediction

Structural modeling of human cardiac sodium channel pore domain

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

Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation

3D Structure Prediction of Noncoding RNA and Single Stranded DNA

A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

Multistable states in a system of coupled phase oscillators with inertia

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Using 3dRPC for RNA–protein complex structure prediction

Types and concentrations of metal ions affect local structure and dynamics of RNA

Dynamics in the Kuramoto model with a bi-harmonic coupling function

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

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

Computational evidence that fast translation speed can increase the probability of cotranslational protein folding

Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

A fast tomographic method for searching the minimum free energy path

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

Efficiently finding the minimum free energy path from steepest descent path

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

How to Use Not-Always-Reliable Binding Site Information in Protein-Protein Docking Prediction

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

Binding free-energy calculation of an ion-peptide complex by constrained dynamics

A novel protocol for three-dimensional structure prediction of RNA-protein complexes

Simulation study of the role of the ribosomal exit tunnel on protein folding

Free-energy calculations along a high-dimensional fragmented path with constrained dynamics

Preorientation of protein and RNA just before contacting

Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath

Effects of Mutation, Truncation, and Temperature on the Folding Kinetics of a WW Domain

Network approach to identify the folding transition states of peptides and proteins

Automated and fast building of three-dimensional RNA structures

生物大分子的自由能计算方法(英文)

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

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure

ASPDock: protein-protein docking algorithm using atomic solvation parameters model

The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel

Free Energy Calculation Methods of Biomolecules

Multi-nucleation and vectorial folding pathways of large helix protein

Symmetric Key Structural Residues in Symmetric Proteins with Beta-Trefoil Fold

Improvements of network approach for analysis of the folding free‐energy surface of peptides and proteins

RNA分子动力学模拟中不同AMBER分子力场与溶剂模型匹配的研究

United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding

Accurate free energy calculation along optimized paths

Folding Mechanism of Beta-Hairpin Trpzip2: Heterogeneity, Transition State and Folding Pathways

Foldable subunits of helix protein

STUDY OF FOLDING BEHAVIORS OF A SIX-HELIX PROTEIN BY ab initio MOLECULAR DYNAMICS FOLDING SIMULATIONS OF UNRES

Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field