Publications

2017

Xiaofeng Ji, Yi Xiao & Shiyong Liu
Structural modeling of human cardiac sodium channel pore domain
Journal of Biomolecular Structure and Dynamics [PubMed] [PDF]

Ran Zhang, Chuangang Liu, Yunzi Cao, Muhammad Jamal, Xi Chen, Jinfang Zheng, Liang Li1, Jing You, Qi Zhu, Shiyong Liu, Jinxia Dai, Min Cui, Zhen F. Fu, Gang Cao
Rabies viruses leader RNA interacts with host Hsc70 and inhibits virus replication
oncotarget [PubMed] [PDF]

2016

Xiaoli Zhang and Shiyong Liu*
RBPPred: predicting RNA-binding proteins from sequence
Bioinformatics December 19, 2016 [abstract]
*Corresponding author
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Jinfang Zheng, Petras J.Kundrotas, Ilya A.V akser* and Shiyong Liu*
Template-based modeling of protein-RNA interactions
PLOS Computational Biology 2016 Sep 23;12(9)[PubMed] [PDF]
*Corresponding author
source download

2014

Hao Chen$, Yunjie Zhao$, Haotian Li$, Dongyan Zhang, Yanzhao Huang, Qi Shen, Rachel Van Duyne, Fatah Kashanchi, Chen Zeng and Shiyong Liu*
Break CDK2/Cyclin E1 Interface Allosterically With Small Peptides
PLOS One 2014 Oct 7; 9(10) [PubMed][PDF]
$ Co-first author *Corresponding author

2013

Xiufeng Yang, Haotian Li, Yangyu Huang, Shiyong Liu*
The dataset for protein-RNA binding affinity
Protein Science. 2013 Dec 1;12:1808-1811. [PubMed] [PDF]
*Corresponding author

Yangyu Huang*, Shiyong Liu*, Dachuan Guo, Lin Li, Yi Xiao
A novel protocol for three-dimensional structure prediction of RNA-protein complexes
Scientific reports May 28;3:1887 [PubMed] [PDF]
*Co-first author

Y Yang, L Luo, J Xu, P Zhu, W Xue, J Wang, W Li, M Wang, K Cheng, S Liu, Z Tang, BZ Ring, L Su
Novel EDA p. Ile260Ser Mutation Linked to Non-syndromic Hypodontia
Journal of dental research Jun 1; 5:500-6
[PDF]

Rocco Moretti, Sarel J Fleishman, Rudi Agius, Mieczyslaw Torchala, Paul A Bates, Panagiotis L Kastritis, Joao PGLM Rodrigues, Mikael Trellet, Alexandre MJJ Bonvin, Meng Cui, Marianne Rooman, Dimitri Gillis, Yves Dehouck, Iain Moal, Miguel Romero-Durana, Laura Perez-Cano, Chiara Pallara, Brian Jimenez, Juan Fernandez-Recio, Samuel Flores, Michael Pacella, Krishna Praneeth Kilambi, Jeffrey J Gray, Petr Popov, Sergei Grudinin, Juan Esquivel-Rodriguez, Daisuke Kihara, Nan Zhao, Dmitry Korkin, Xiaolei Zhu, Omar NA Demerdash, Julie C Mitchell, Eiji Kanamori, Yuko Tsuchiya, Haruki Nakamura, Hasup Lee, Hahnbeom Park, Chaok Seok, Jamica Sarmiento, Shide Liang, Shusuke Teraguchi, Daron M Standley, Hiromitsu Shimoyama, Genki Terashi, Mayuko Takeda‐Shitaka, Mitsuo Iwadate, Hideaki Umeyama, Dmitri Beglov, David R Hall, Dima Kozakov, Sandor 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 Velankar, Joel Janin, Shoshana J Wodak, David Baker
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
Proteins. 2013 Nov 1; 11:1980-7 [PubMed]

2012

Yang-Yu HUANG, Xiu-Feng YANG, Hao-Tian LI, Xiao-Feng JI, Hong-Li CHENG, Yun-Jie ZHAO, Da-Chuan GUO, Lin LI, Shi-Yong LIU*
Protein-RNA Interaction Interface Prediction and Design
Acta Physico-Chimica Sinica 2012 Sep 11; 8(10): 2390-2400 [PDF] * Corresponding author

Dachuan Guo*, Shiyong Liu*, Yangyu Huang, Yi Xiao Preorientation of protein and RNA just before contacting
Journal of Biomolecular Structure and Dynamics 2012 Jan 1; 1-13
[PubMed] [PDF]
*Co-first author

2011

Shiyong Liu, Ilya Vakser
DECK: Distance-scale environment-dependent coarse-grained knowledge-based potentials for protein-protein docking
BMC Bioinformatics 2011 Jul 11; 12:280.
[PubMed] [PDF]

Lin Li, Dachuan Guo, Yangyu Huang, Shiyong Liu* and Yi Xiao*
ASPDock: protein-protein docking algorithm using atomic solvation parameters model
BMC Bioinformatics. 2011 Jan 27;12:36.
[PubMed] [PDF]
* Co-Corresponding author

Sarel J Fleishman, Timothy A Whitehead, Eva-Maria Strauch, Jacob E Corn, Sanbo Qin, Huan-Xiang Zhou, Julie C Mitchell, Omar NA 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, Jerome Aze, Seren Soner, Sefik Kerem Ovalı, Pemra Ozbek, Nir Ben Tal, Turkan Haliloglu, Howook Hwang, Thom Vreven, Brian G Pierce, Zhiping Weng, Laura Perez-Cano, Carles Pons, Juan Fernandez-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, Dachuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Itzhaki, Ora Schueler-Furman, Yuval Inbar, Vladimir Potapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M Standley, Haruki Nakamura, Kengo Kinoshita, Camden M Driggers, Robert G Hall, Jessica L Morgan, Victor L Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L Kastritis, Alexandre MJJ Bonvin, Weiyi Zhang, Carlos J Camacho, Krishna P Kilambi, Aroop Sircar, Jeffrey J Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel-Rodriguez, Daisuke Kihara, P Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J Wodak, Joel Janin, David Baker
Community-wide assessment of protein-interface modeling suggests improvements to design methodology Journal of molecular biology 2011 Nov 25; 2:289-302.
[PDF]

2008

Shiyong Liu, Ying Gao and Ilya A. Vakser
DOCKGROUND protein-protein docking decoy set.
Bioinformatics.2008 Sep 23; [PubMed][PDF]

Lu Zhou, Chao Fang, Ping Wei, Shiyong Liu, Ying Liu, and Luhua Lai
Chemically Induced Dimerization of Human Nonpancreatic Secretory Phospholipase A2 by Bis-indole Derivatives
J. Med. Chem. 2008 June 4; [PubMed][PDF]

2007

Hongjun Bai, Wenzhe Ma, Shiyong Liu, Luhua Lai
Dynamic property is a key determinant for protein-protein interactions.
Proteins. 2007 Sep 17; [PubMed][PDF]

Sen liu*, Shiyong Liu*, Xiaolei Zhu, Huanhuan Liang, Aoneng Cao, Zhijie Chang, and Luhua Lai
Nonnatural protein-protein interaction-pair design by key residues grafting.
Pnas. 2007 104(13):5330-35. [PubMed][PDF]
* Co-first author

2006

Lai, Luhua; Han, Xiaofeng; Chen, Hao; Wei, Ping; Huang, Changkang; Liu, Shiyong; Fan, Keqiang; Zhou, Lu; Liu, Zhenming; Pei, Jianfeng; Liu, Ying
Quaternary structure, substrate selectivity and inhibitor design for SARS 3C-like proteinase.Curr Pharm Des.
Curr Pharm Des. 2006 12(35):4555-64. [PubMed][PDF]

Shiyong Liu, Qingliang Li and Luhua Lai
A combinatorial score to distinguish biological and non-biological protein-protein interfaces
Proteins 2006 64(1):68-78. [PubMed][PDF]

2005

Liu Z, Huang C, Fan K, Wei P, Chen H, Liu S, Pei J, Shi L, Li B, Yang K, Liu Y, Lai L.
Virtual Screening of Novel Noncovalent Inhibitors for SARS-CoV 3C-like Proteinase
J Chem Inf Comput Sci. 2005 45(1):10-7. [PubMed] [PDF]

2003

Liu S*, Pei J*, Chen H*, Zhu X, Liu Z, Ma W, He F, Lai L.
Modeling of the SARS coronavirus main proteinase and conformational flexibility of the active site
Beijing Da Xue Xue Bao. 2003 31;35 Suppl:62-5. Chinese. [PubMed][PDF]

* Co-first author
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