Wei Zheng
Wei Zheng
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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