Chengxin Zhang

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 52

Top Topics

Crystal Structure

Top Venues

bioRxiv : the preprint server for biology

Nature communications

Journal of proteome research

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

Publications

Xiaoqiong Wei, You Lu, Liangguang Leo Lin, Chengxin Zhang, Xinxin Chen, Siwen Wang, Shuangcheng Alivia Wu, Zexin Jason Li, Yujun Quan, Shengyi Sun, Ling Qi
Proteomic screens of SEL1L-HRD1 ER-associated degradation substrates reveal its role in glycosylphosphatidylinositol-anchored protein biogenesis. Nature communications 15 (1) (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Chengxin Zhang, Peter L Freddolino
A large-scale assessment of sequence database search tools for homology-based protein function prediction. Briefings in bioinformatics 25 (4) (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)
Chengxin Zhang, Peter L Freddolino
A large-scale assessment of sequence database search tools for homology-based protein function prediction. Briefings in bioinformatics 25 (4) (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Xiaoqiong Wei, You Lu, Liangguang Leo Lin, Chengxin Zhang, Xinxin Chen, Siwen Wang, Shuangcheng Alivia Wu, Zexin Jason Li, Yujun Quan, Shengyi Sun, Ling Qi
Proteomic screens of SEL1L-HRD1 ER-associated degradation substrates reveal its role in glycosylphosphatidylinositol-anchored protein biogenesis. Nature communications 15 (1) (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Xiaoqiong Wei, You Lu, Liangguang Leo Lin, Chengxin Zhang, Xinxin Chen, Siwen Wang, Shuangcheng Alivia Wu, Zexin Jason Li, Yujun Quan, Shengyi Sun, Ling Qi
Proteomic screens of SEL1L-HRD1 ER-associated degradation substrates reveal its role in glycosylphosphatidylinositol-anchored protein biogenesis. Nature communications 15 (1) (2024)
Xiaoqiong Wei, You Lu, Liangguang Leo Lin, Chengxin Zhang, Xinxin Chen, Siwen Wang, Shuangcheng Alivia Wu, Zexin Jason Li, Yujun Quan, Shengyi Sun, Ling Qi
Proteomic screens of SEL1L-HRD1 ER-associated degradation substrates reveal its role in glycosylphosphatidylinositol-anchored protein biogenesis. Nature communications 15 (1) (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)
Xiaoqiong Wei, You Lu, Liangguang Leo Lin, Chengxin Zhang, Xinxin Chen, Siwen Wang, Shuangcheng Alivia Wu, Zexin Jason Li, Yujun Quan, Shengyi Sun, Ling Qi
Proteomic screens of SEL1L-HRD1 ER-associated degradation substrates reveal its role in glycosylphosphatidylinositol-anchored protein biogenesis. Nature communications 15 (1) (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)
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)
Chengxin Zhang, Peter L Freddolino
FURNA: A database for functional annotations of RNA structures. PLoS biology 22 (7) (2024)
Chengxin Zhang, Peter L Freddolino
A large-scale assessment of sequence database search tools for homology-based protein function prediction. Briefings in bioinformatics 25 (4) (2024)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Christopher T A Lewis, Elise G Melhedegaard, Marija M Ognjanovic, Mathilde S Olsen, Jenni Laitila, Robert A E Seaborne, Magnus Nørregaard Grønset, Chengxin Zhang, Hiroyuki Iwamoto, Anthony L Hessel, Michel N Kuehn, Carla Merino, Nuria Amigó, Ole Fröbert, Sylvain Giroud, James F Staples, Anna V Goropashnaya, Vadim B Fedorov, Brian M Barnes, Øivind Tøien, Kelly L Drew, Ryan J Sprenger, Sylvain Giroud
Remodelling of skeletal muscle myosin metabolic states in hibernating mammals. bioRxiv : the preprint server for biology (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)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Anna Marie Pyle
PDC: a highly compact file format to store protein 3D coordinates. Database : the journal of biological databases and curation 2023 (2023)
Chengxin Zhang, Peter L Freddolino
A large-scale assessment of sequence database search tools for homology-based protein function prediction. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Yuxuan Song, Chengxin Zhang, Gilbert S Omenn, Matthew J O'Meara, Joshua D Welch
Predicting the Structural Impact of Human Alternative Splicing. bioRxiv : the preprint server for biology (2023)
Yuxuan Song, Chengxin Zhang, Gilbert S Omenn, Matthew J O'Meara, Joshua D Welch
Predicting the Structural Impact of Human Alternative Splicing. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Yuxuan Song, Chengxin Zhang, Gilbert S Omenn, Matthew J O'Meara, Joshua D Welch
Predicting the Structural Impact of Human Alternative Splicing. bioRxiv : the preprint server for biology (2023)
Chengxin Zhang, Peter L Freddolino
FURNA: a database for function annotations of RNA structures. bioRxiv : the preprint server for biology (2023)
Longlong Si, Quan Shen, Jing Li, Li Chen, Jinying Shen, Xue Xiao, Haiqing Bai, Tang Feng, Adam Yongxin Ye, Le Li, Chunhe Zhang, Zhen Li, Ping Wang, Crystal Yuri Oh, Atiq Nurani, Siwen Niu, Chengxin Zhang, Xiaoqiong Wei, Wanqiong Yuan, Hao Liao, Xiaojie Huang, Ning Wang, Wen-Xia Tian, Hongwei Tian, Li Li, Xiaoheng Liu, Roberto Plebani
Generation of a live attenuated influenza A vaccine by proteolysis targeting. Nature biotechnology 40 (9) (2022)
Chengxin Zhang, Anna Marie Pyle
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures. Acta crystallographica. Section D, Structural biology 78 (Pt 4) (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)
Morgan Shine, Chengxin Zhang, Anna Marie Pyle
AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. Bioinformatics (Oxford, England) 38 (10) (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)
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)
Jian Chang, Chengxin Zhang, Huaqiang Cheng, Yan-Wen Tan
Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis. International journal of molecular sciences 22 (5) (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)
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)
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)
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)
Shaolei Wang, Chengxin Zhang, Yu Shu, Shulan Jiang, Qi Xia, Linjiang Chen, Shangbin Jin, Irshad Hussain, Andrew I Cooper, Bien Tan
Layered microporous polymers by solvent knitting method. Science advances 3 (3) (2017)