Yang Zhang

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 60

Top Topics

Protein Protein

Top Venues

PLoS computational biology

Proceedings of the National Academy of Sciences of the United States of America

Journal of chemical information and modeling

This page only lists publications with an associated author ORCID identifier.

Publications

Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling 64 (3) (2024)
Wei Zheng, Qiqige Wuyun, Yang Zhang
One step forward towards deep-learning protein complex structure prediction by precise multiple sequence alignment construction. Clinical and translational medicine 14 (6) (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling (2024)
Wei Zheng, Qiqige Wuyun, Yang Zhang
One step forward towards deep-learning protein complex structure prediction by precise multiple sequence alignment construction. Clinical and translational medicine 14 (6) (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling 64 (3) (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods 21 (2) (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling 64 (3) (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods 21 (2) (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of chemical information and modeling 64 (3) (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods 21 (2) (2024)
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature methods 21 (2) (2024)
Robin Pearce, Xiaoqiang Huang, Gilbert S Omenn, Yang Zhang
De novo protein fold design through sequence-independent fragment assembly simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Chengxin Zhang, Xi Zhang, Peter L Freddolino, Yang Zhang
BioLiP2: an updated structure database for biologically relevant ligand-protein interactions. Nucleic acids research (2023)
Yang Li, Chengxin Zhang, Chenjie Feng, Robin Pearce, Peter L Freddolino, Yang Zhang
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction. Nature communications 14 (1) (2023)
Robin Pearce, Xiaoqiang Huang, Gilbert S Omenn, Yang Zhang
De novo protein fold design through sequence-independent fragment assembly simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Robin Pearce, Xiaoqiang Huang, Gilbert S Omenn, Yang Zhang
De novo protein fold design through sequence-independent fragment assembly simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Robin Pearce, Xiaoqiang Huang, Gilbert S Omenn, Yang Zhang
De novo protein fold design through sequence-independent fragment assembly simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Robin Pearce, Xiaoqiang Huang, Gilbert S Omenn, Yang Zhang
De novo protein fold design through sequence-independent fragment assembly simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Xiao-Gen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang
Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nature computational science 2 (4) (2022)
Xi Zhang, Biao Zhang, Peter L Freddolino, Yang Zhang
CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks. Nature methods 19 (2) (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 computational biology 18 (12) (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 computational biology 18 (12) (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 computational biology 18 (12) (2022)
Robin Pearce, Yang Li, Gilbert S Omenn, Yang Zhang
Fast and accurate Ab Initio Protein structure prediction using deep learning potentials. PLoS computational biology 18 (9) (2022)
Haifeng Zhang, Renjie Shang, Kwantae Kim, Wei Zheng, Christopher J Johnson, Lei Sun, Xiang Niu, Liang Liu, Jingqi Zhou, Lingshu Liu, Zheng Zhang, Theodore Akira Uyeno, Jimin Pei, Skye D Fissette, Stephen A Green, Sukhada P Samudra, Junfei Wen, Jianli Zhang, Jonathan T Eggenschwiler, Douglas B Menke, Marianne E Bronner, Nick V Grishin, Weiming Li, Kaixiong Ye, Yang Zhang, Travis M Rotterman, Pengpeng Bi
Evolution of a chordate-specific mechanism for myoblast fusion. Science advances 8 (35) (2022)
Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature methods 19 (9) (2022)
Xiao-Gen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Gui-Jun Zhang, Yang Zhang
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic acids research (2022)
Xiao-Gen Zhou, Wei Zheng, Yang Li, Robin Pearce, Chengxin Zhang, Eric W Bell, Guijun Zhang, Yang Zhang
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction. Nature protocols 17 (10) (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 computational biology 18 (12) (2022)
Pengshuo Yang, Wei Zheng, Kang Ning, Yang Zhang
Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America 118 (49) (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 computational biology 18 (12) (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 research (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 computational biology 18 (12) (2022)
Wei Zheng, Yang Li, Chengxin Zhang, Xiao-Gen Zhou, Robin Pearce, Eric W Bell, Xiaoqiang Huang, Yang Zhang
Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. Proteins 89 (12) (2021)
Chengxin Zhang, Wei Zheng, Micah Cheng, Gilbert S Omenn, Peter L Freddolino, Yang Zhang
Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. Journal of proteome research 20 (2) (2021)
Yang Li, Chengxin Zhang, Eric W Bell, Wei Zheng, Xiao-Gen Zhou, Dong-Jun Yu, Yang Zhang
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS computational biology 17 (3) (2021)
Biao Zhang, Wenyi Zhang, Robin Pearce, Yang Zhang, Hong-Bin Shen
Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations. The journal of physical chemistry. B 125 (2) (2021)
Yang Li, Chengxin Zhang, Wei Zheng, Xiao-Gen Zhou, Eric W Bell, Dong-Jun Yu, Yang Zhang
Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. Proteins 89 (12) (2021)
S M Mortuza, Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Yang Zhang
Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature communications 12 (1) (2021)
Jaie Woodard, Wei Zheng, Yang Zhang
Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. PLoS computational biology 17 (9) (2021)
Xiao-Gen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang
Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps. bioRxiv : the preprint server for biology (2020)
Wenyi Zhang, Eric W Bell, Minghao Yin, Yang Zhang
EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. Journal of cheminformatics 12 (1) (2020)
Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W Bell, Xiao-Gen Zhou, Yang Zhang
Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. Journal of proteome research 19 (4) (2020)
Xiaoqiang Huang, Chengxin Zhang, Robin Pearce, Gilbert S Omenn, Yang Zhang
Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2. Journal of proteome research 19 (12) (2020)
Wei Zheng, Yang Li, Chengxin Zhang, Robin Pearce, S M Mortuza, Yang Zhang
Deep-learning contact-map guided protein structure prediction in CASP13. Proteins 87 (12) (2019)
Xiaoqiang Huang, Robin Pearce, Yang Zhang
Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. Journal of chemical information and modeling 60 (1) (2019)
Eric W Bell, Yang Zhang
DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. Journal of cheminformatics 11 (1) (2019)
Yan Wang, Qiang Shi, Pengshuo Yang, Chengxin Zhang, S M Mortuza, Zhidong Xue, Kang Ning, Yang Zhang
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families. Genome biology 20 (1) (2019)
Chengxin Zhang, Lydie Lane, Gilbert S Omenn, Yang Zhang
Blinded Testing of Function Annotation for uPE1 Proteins by I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge. Journal of proteome research 18 (12) (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 computational biology 15 (10) (2019)
Xiao-Gen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, Yang Zhang
Assembling multidomain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences of the United States of America 116 (32) (2019)
Yang Li, Chengxin Zhang, Eric W Bell, Dong-Jun Yu, Yang Zhang
Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13. Proteins 87 (12) (2019)
Chengxin Zhang, Xiaoqiong Wei, Gilbert S Omenn, Yang Zhang
Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17. Journal of proteome research 17 (12) (2018)
Jouko J Virtanen, Yang Zhang
MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models. Acta crystallographica. Section D, Structural biology 74 (Pt 7) (2018)
Jun Hu, Yang Li, Yang Zhang, Dong-Jun Yu
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. Journal of chemical information and modeling 58 (2) (2018)
Jens M H Thomas, Felix Simkovic, Ronan Keegan, Olga Mayans, Chengxin Zhang, Yang Zhang, Daniel J Rigden
Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta crystallographica. Section D, Structural biology 73 (Pt 12) (2017)
Chengxin Zhang, S M Mortuza, Baoji He, Yanting Wang, Yang Zhang
Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins (2017)
Mary Ashley Rimmer, Owen W Nadeau, Jianyi Yang, Antonio Artigues, Yang Zhang, Gerald M Carlson
The structure of the large regulatory α subunit of phosphorylase kinase examined by modeling and hydrogen-deuterium exchange. Protein science : a publication of the Protein Society 27 (2) (2017)
Ismaila O Nurain, Clement O Bewaji, Jarrett S Johnson, Robertson D Davenport, Yang Zhang
Potential of Three Ethnomedicinal Plants as Antisickling Agents. Molecular pharmaceutics 14 (1) (2016)