| Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations W Zheng, C Zhang, Y Li, R Pearce, EW Bell, Y Zhang Cell reports methods 1 (3), 2021 | 367 | 2021 |
| 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 C Zhang, W Zheng, X Huang, EW Bell, X Zhou, Y Zhang Journal of proteome research 19 (4), 1351-1360, 2020 | 360 | 2020 |
| Deep‐learning contact‐map guided protein structure prediction in CASP13 W Zheng, Y Li, C Zhang, R Pearce, SM Mortuza, Y Zhang Proteins: Structure, Function, and Bioinformatics 87 (12), 1149-1164, 2019 | 205 | 2019 |
| DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins C Zhang, W Zheng, SM Mortuza, Y Li, Y Zhang Bioinformatics 36 (7), 2105-2112, 2020 | 150 | 2020 |
| LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins W Zheng, C Zhang, Q Wuyun, R Pearce, Y Li, Y Zhang Nucleic acids research 47 (W1), W429-W436, 2019 | 139 | 2019 |
| I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction X Zhou, W Zheng, Y Li, R Pearce, C Zhang, EW Bell, G Zhang, Y Zhang Nature Protocols 17 (10), 2326-2353, 2022 | 136 | 2022 |
| BindProfX: assessing mutation-induced binding affinity change by protein interface profiles with pseudo-counts P Xiong, C Zhang, W Zheng, Y Zhang Journal of molecular biology 429 (3), 426-434, 2017 | 118 | 2017 |
| Effects of SARS‐CoV‐2 mutations on protein structures and intraviral protein–protein interactions S Wu, C Tian, P Liu, D Guo, W Zheng, X Huang, Y Zhang, L Liu Journal of medical virology 93 (4), 2132-2140, 2021 | 106 | 2021 |
| I-TASSER gateway: A protein structure and function prediction server powered by XSEDE W Zheng, C Zhang, EW Bell, Y Zhang Future Generation Computer Systems 99, 73-85, 2019 | 104 | 2019 |
| Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks Y Li, C Zhang, EW Bell, W Zheng, X Zhou, DJ Yu, Y Zhang PLoS computational biology 17 (3), e1008865, 2021 | 81 | 2021 |
| MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein–protein network mapping C Zhang, W Zheng, PL Freddolino, Y Zhang Journal of molecular biology 430 (15), 2256-2265, 2018 | 71 | 2018 |
| Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions SM Mortuza, W Zheng, C Zhang, Y Li, R Pearce, Y Zhang Nature communications 12 (1), 5011, 2021 | 58 | 2021 |
| Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14 W Zheng, Y Li, C Zhang, X Zhou, R Pearce, EW Bell, X Huang, Y Zhang Proteins: Structure, Function, and Bioinformatics 89 (12), 1734-1751, 2021 | 56 | 2021 |
| Cryo-EM structure of the human MLL1 core complex bound to the nucleosome SH Park, A Ayoub, YT Lee, J Xu, H Kim, W Zheng, B Zhang, L Sha, S An, ... Nature communications 10 (1), 5540, 2019 | 56 | 2019 |
| Detecting distant-homology protein structures by aligning deep neural-network based contact maps W Zheng, Q Wuyun, Y Li, SM Mortuza, C Zhang, R Pearce, J Ruan, ... PLoS computational biology 15 (10), e1007411, 2019 | 50 | 2019 |
| FUpred: detecting protein domains through deep-learning-based contact map prediction W Zheng, X Zhou, Q Wuyun, R Pearce, Y Li, Y Zhang Bioinformatics 36 (12), 3749-3757, 2020 | 48 | 2020 |
| SSIPe: accurately estimating protein–protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function X Huang, W Zheng, R Pearce, Y Zhang Bioinformatics 36 (8), 2429-2437, 2020 | 43 | 2020 |
| Improved species-specific lysine acetylation site prediction based on a large variety of features set Q Wuyun, W Zheng, Y Zhang, J Ruan, G Hu PloS one 11 (5), e0155370, 2016 | 36 | 2016 |
| Progressive assembly of multi-domain protein structures from cryo-EM density maps X Zhou, Y Li, C Zhang, W Zheng, G Zhang, Y Zhang Nature computational science 2 (4), 265-275, 2022 | 34 | 2022 |
| A large-scale comparative assessment of methods for residue–residue contact prediction Q Wuyun, W Zheng, Z Peng, J Yang Briefings in bioinformatics 19 (2), 219-230, 2018 | 33 | 2018 |
