Chengxin Zhang

发表

Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14

Eric W. Bell, Yang Zhang, Dong-Jun Yu, 2021, Proteins.

MetaGO : Predict Non-homologou Low-Resolution Prediction and P Network Mappin

Yang Zhang, Chengxin Zhang, Wei Zheng, 2018 .

MetaGO : Predicting Gene Ontology of Non-hom Resolutio Protein – P

Peter L. Freddolino, Yang Zhang, Chengxin Zhang, 2018 .

Gut Fungi Possess a Conserved Toxin Immunity Gene of Bacterial Origin

Peter L. Freddolino, Yang Zhang, Syed M. Rizvi, 2020, bioRxiv.

Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1

Eric W. Bell, Yang Zhang, Xiaoqiang Huang, 2020, bioRxiv.

Generation of a live attenuated influenza A vaccine by proteolysis targeting

A. Y. Ye, Zhuguo Li, Quan Shen, 2022, Nature Biotechnology.

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction

Peter L. Freddolino, G. Omenn, Yang Zhang, 2022, Genom. Proteom. Bioinform..

Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps

Yang Zhang, Yang Li, Chengxin Zhang, 2020, bioRxiv.

Identifying zoonotic origin of SARS-CoV-2 by modeling the binding affinity between Spike receptor-binding domain and host ACE2

Yang Zhang, G. Omenn, Xiaoqiang Huang, 2020, bioRxiv.

Controlling Monomer Feeding Rate to Achieve Highly Crystalline Covalent Triazine Frameworks

Buyin Li, Hao Chen, B. Tan, 2019, Advanced materials.

Integrating Self-Attention Transformer with Triplet Neural Networks for Protein Gene Ontology Prediction

Yang Zhang, Dong-Jun Yu, Chengxin Zhang, 2022, bioRxiv.

Approaches to ab initio molecular replacement of α-helical transmembrane proteins

O. Mayans, Yang Zhang, D. Rigden, 2017, Acta crystallographica. Section D, Structural biology.

Soluble CD13 induces inflammatory arthritis by activating the bradykinin receptor B1

A. Urquhart, Chenyang Lu, T. Maerz, 2022, The Journal of clinical investigation.

AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids

A. Pyle, Chengxin Zhang, Morgan Shine, 2022, Bioinformatics.

Deep learning geometrical potential for high-accuracy ab initio protein structure prediction

Yang Zhang, Dong-Jun Yu, Yang Li, 2022, iScience.

I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction

Eric W. Bell, Robin Pearce, Guijun Zhang, 2022, Nature Protocols.

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks

Eric W. Bell, Yang Zhang, Dong-Jun Yu, 2020, bioRxiv.

rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling.

Yang Zhang, Chengxin Zhang, A. Marie Pyle, 2022, Journal of molecular biology.

Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families

Yang Zhang, Z. Xue, S. Mortuza, 2019, Genome Biology.

BeEM: fast and faithful conversion of mmCIF format structure files to PDB format

Chengxin Zhang, 2022, bioRxiv.

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

Yang Zhang, Peter L. Freddolino, Chengxin Zhang, 2017, Nucleic Acids Res..

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE

Wei Zheng, Chengxin Zhang, Yang Zhang, 2019, Future Gener. Comput. Syst..

Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion

Xiaoyan Ke, Yang Zhang, Qin Yin, 2019, ACS omega.

Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations

Eric W. Bell, Yang Zhang, Robin Pearce, 2021, Cell reports methods.

Assembling multidomain protein structures through analogous global structural alignments

Xiaogen Zhou, Yang Zhang, Jun Hu, 2019, Proceedings of the National Academy of Sciences.

US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes

A. Pyle, Chengxin Zhang, Yang Zhang, 2022, Nature Methods.

ADDRESS: A database of disease-associated human variants incorporating protein structure and folding stabilities.

Yang Zhang, Chengxin Zhang, Jaie C. Woodard, 2021, Journal of molecular biology.

Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14

Eric W. Bell, Yang Zhang, Xiaoqiang Huang, 2021, Proteins.

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

Eric W. Bell, Yang Zhang, Yang Zhang, 2020, Journal of proteome research.

RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control

Yang Zhang, H. Paulson, L. Sharkey, 2021, Cellular and Molecular Life Sciences.

Computational analysis of vertebrate myoglobins reveals aggregation resistance in aquatic birds and higher surface hydrophobicity in fish

Yang Zhang, Syed M. Rizvi, Chengxin Zhang, 2021 .

Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2

Yang Zhang, G. Omenn, Xiaoqiang Huang, 2020, Journal of proteome research.

Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions

Yang Zhang, Robin Pearce, S. Mortuza, 2021, Nature Communications.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

Ensembling multiple raw coevolutionary features with deep residual neural networks for contact‐map prediction in CASP13

Yang Zhang, Yang Li, Dong-Jun Yu, 2019, Proteins.

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks

Jun Hu, Yang Zhang, Yang Li, 2019, Bioinform..

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins

Yang Zhang, Wei Zheng, Yang Li, 2019, Bioinform..

Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli

Yang Zhang, Weikang Gong, Aysam Guerler, 2020, bioRxiv.

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

Yang Zhang, Peter L. Freddolino, Wei Zheng, 2018, Journal of molecular biology.

PyMod 2.0: improvements in protein sequence‐structure analysis and homology modeling within PyMOL

Chengxin Zhang, Giacomo Janson, Alessandro Paiardini, 2016, Bioinform..

hiPSC Modeling of Lineage-Specific Smooth Muscle Cell Defects Caused by TGFBR1A230T Variant, and Its Therapeutic Implications for Loeys-Dietz Syndrome

Y. E. Chen, Dong Zhou, P. Qiu, 2021, Circulation.

Detecting distant-homology protein structures by aligning deep neural-network based contact maps

Yang Zhang, Wei Zheng, Robin Pearce, 2019, PLoS Comput. Biol..

Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.

Peter L. Freddolino, Yang Zhang, G. Omenn, 2021, Journal of proteome research.

EDIL3 deficiency ameliorates adverse cardiac remodeling by neutrophil extracellular traps (NET)-mediated macrophage polarization.

Yuquan Wei, Zhenyu Chen, Yifan Zhou, 2021, Cardiovascular research.

PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL.

A. Paiardini, G. Janson, Chengxin Zhang, 2016, Bioinformatics.

BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts.

Wei Zheng, Yang Zhang, Chengxin Zhang, 2017, Journal of molecular biology.

Deep‐learning contact‐map guided protein structure prediction in CASP13

Yang Zhang, Wei Zheng, Yang Li, 2019, Proteins.

Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1

Xiaogen Zhou, Yang Zhang, Wei Zheng, 2020, bioRxiv.

A Blinded Testing of Function Annotation for uPE1 Proteins by the I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge.

Lydie Lane, Yang Zhang, Chengxin Zhang, 2019, Journal of proteome research.

Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17.

Yang Zhang, Chengxin Zhang, Gilbert S Omenn, 2018, Journal of proteome research.

Evolution of myoglobin in avian lineages: positive selection for aggregation resistance in penguins and high purifying selection in galliforms

Syed M. Rizvi, Chengxin Zhang, Wei Zheng, 2022, bioRxiv.

Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction

Yang Zhang, Dong-Jun Yu, Chengxin Zhang, 2022, PLoS Comput. Biol..

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for High-Accuracy Gene Function Annotations

Peter L. Freddolino, Yang Zhang, G. Omenn, 2021, bioRxiv.

Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction

Peter L. Freddolino, Yang Zhang, Yang Li, 2022, bioRxiv.

RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA

Yang Zhang, Chengxin Zhang, Sha Gong, 2019, Bioinform..

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks

Xiaogen Zhou, Yang Zhang, Chengxin Zhang, 2020, bioRxiv.

Progressive assembly of multi-domain protein structures from cryo-EM density maps

W. Zheng, G. Zhang, Y. Zhang, 2022, Nature Computational Science.

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins

Yang Li, Wei Zheng, Qiqige Wuyun, 2019, Nucleic Acids Res..

Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli

Yang Zhang, Chunhua Li, Aysam Guerler, 2020, bioRxiv.

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

Yang Zhang, Chengxin Zhang, Baoji He, 2018, Proteins.

Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis

Yan-Wen Tan, Jian Chang, Chengxin Zhang, 2021, International journal of molecular sciences.

Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families

Yan Wang, Kang Ning, Yang Zhang, 2019, Genome Biology.

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons

Zhiyong Lu, Yang Zhang, Peter L. Freddolino, 2020, Bioinform..

A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs

Chengxin Zhang, A. M. Pyle, 2022, iScience.

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE

Eric W. Bell, Yang Zhang, Chengxin Zhang, 2019, Future Gener. Comput. Syst..

Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17.

Yang Zhang, Chengxin Zhang, Xiaoqiong Wei, 2018, Journal of Proteome Research.

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

Yang Zhang, Yanting Wang, S. Mortuza, 2018, Proteins.

Proteomic screens of SEL1L-HRD1 ER-associated degradation substrates reveal its role in glycosylphosphatidylinositol-anchored protein biogenesis

Chengxin Zhang, Shengyi Sun, Xiaoqiong Wei, 2024, Nature communications.

BioLiP2: an updated structure database for biologically relevant ligand–protein interactions

Yang Zhang, Chengxin Zhang, Xi Zhang, 2023, Nucleic acids research.

Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data

Yang Li, Chengxin Zhang, Wei Zheng, 2024, Nature methods.

PDC: a highly compact file format to store protein 3D coordinates

A. Pyle, Chengxin Zhang, 2023, Database J. Biol. Databases Curation.

Remodelling of skeletal muscle myosin metabolic states in hibernating mammals

J. F. Staples, A. Hessel, Chengxin Zhang, 2023, bioRxiv.

PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL

A. Paiardini, G. Janson, Chengxin Zhang, 2017, Bioinform..