Yang Zhang

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 24

Top Topics

Protein Structure

Bayes Classifiers

Sequence Alignment

Top Venues

Nucleic Acids Res.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. J. Chem. Inf. Model. 64 (3) (2024)
Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang
Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nat. Comput. Sci. 2 (4) (2022)
Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Res. 50 (W1) (2022)
Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Peter L. Freddolino, Yang Zhang
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic Acids Res. 50 (W1) (2022)
Yi-Heng Zhu, Chengxin Zhang, Yan Liu, Gilbert S. Omenn, Peter L. Freddolino, Dong-Jun Yu, Yang Zhang
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction. Genom. Proteom. Bioinform. 20 (5) (2022)
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS Comput. Biol. 18 (12) (2022)
Yang Li, Chengxin Zhang, Eric W. Bell, Wei Zheng, Xiaogen Zhou, Dong-Jun Yu, Yang Zhang
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS Comput. Biol. 17 (3) (2021)
Xiaogen Zhou, Chunxiang Peng, Jun Liu, Yang Zhang, Gui-Jun Zhang
Underestimation-Assisted Global-Local Cooperative Differential Evolution and the Application to Protein Structure Prediction. IEEE Trans. Evol. Comput. 24 (3) (2020)
Xiaoqiang Huang, Robin Pearce, Yang Zhang
EvoEF2: accurate and fast energy function for computational protein design. Bioinform. 36 (4) (2020)
Wenyi Zhang, Eric W. Bell, Minghao Yin, Yang Zhang
EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. J. Cheminformatics 12 (1) (2020)
Xiaoqiang Huang, Robin Pearce, Yang Zhang
FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinform. 36 (12) (2020)
Xiaoqiang Huang, Robin Pearce, Yang Zhang
Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. J. Chem. Inf. Model. 60 (1) (2020)
Jun Liu, Xiao-Gen Zhou, Yang Zhang, Gui-Jun Zhang
CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinform. 36 (8) (2020)
Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang
FUpred: detecting protein domains through deep-learning-based contact map prediction. Bioinform. 36 (12) (2020)
Chengxin Zhang, Wei Zheng, S. M. Mortuza, Yang Li, Yang Zhang
DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinform. 36 (7) (2020)
Eric W. Bell, Yang Zhang
DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. J. Cheminformatics 11 (1) (2019)
Wei Zheng, Qiqige Wuyun, Yang Li, S. M. Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, Yang Zhang
Detecting distant-homology protein structures by aligning deep neural-network based contact maps. PLoS Comput. Biol. 15 (10) (2019)
Wei Zheng, Chengxin Zhang, Eric W. Bell, Yang Zhang
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. Future Gener. Comput. Syst. 99 (2019)
Wei Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang
LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Sha Gong, Chengxin Zhang, Yang Zhang
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. Bioinform. 35 (21) (2019)
Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinform. 35 (22) (2019)
Jun Hu, Yang Li, Yang Zhang, Dong-Jun Yu
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. J. Chem. Inf. Model. 58 (2) (2018)
Baoji He, S. M. Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang
NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers. Bioinform. 33 (15) (2017)
Chengxin Zhang, Peter L. Freddolino, Yang Zhang
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Res. 45 (Webserver-Issue) (2017)