Zhang, Chengxin

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

Zhang, C., Freddolino, L., & Zhang, Y. (2017) · Nucleic Acids Research

Protein Structure and DynamicsBioinformatics and Genomic Networks

Cited by 606

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

Zhang, C., Shine, M., Pyle, A. M., & Zhang, Y. (2022) · Nature Methods

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 511

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

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., et al. (2019) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 452

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

Zheng, W., Li, Y., Zhang, C., Pearce, R., Mortuza, S. M., & Zhang, Y. (2019) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 208

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

Li, Y., Hu, J., Zhang, C., Yu, D.-J., & Zhang, Y. (2019) · Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 158

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

Xiong, P., Zhang, C., Zheng, W., & Zhang, Y. (2017) · Journal of Molecular Biology

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 140

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

Li, Y., Zhang, C., Bell, E. W., Yu, D., & Zhang, Y. (2019) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 94

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

Zhang, C., Zheng, W., Freddolino, L., & Zhang, Y. (2018) · Journal of Molecular Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 80

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

Zhou, X., Li, Y., Zhang, C., Zheng, W., Zhang, G., & Zhang, Y. (2022) · Nature Computational Science

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 75

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

Zhang, C., Zheng, W., Cheng, M., Omenn, G. S., Freddolino, P. L., & Zhang, Y. (2021) · Journal of Proteome Research

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 27

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

Zhang, C., Lane, L., Omenn, G. S., & Zhang, Y. (2019) · Journal of Proteome Research

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 22

A large-scale assessment of sequence database search tools for homology-based protein function prediction

Zhang, C., & Freddolino, L. (2024) · Briefings in Bioinformatics

Machine Learning in BioinformaticsBioinformatics and Genomic Networks

Cited by 16

Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli

Gong, W., Guerler, A., Zhang, C., Warner, E., Li, C., & Zhang, Y. (2021) · Journal of Molecular Biology

Protein Structure and DynamicsBioinformatics and Genomic Networks

Cited by 13