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Yang Li
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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
3612021
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
2042019
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks
Y Li, J Hu, C Zhang, DJ Yu, Y Zhang
Bioinformatics 35 (22), 4647-4655, 2019
1532019
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
1482020
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
1382019
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
1292022
Ensembling multiple raw coevolutionary features with deep residual neural networks for contact‐map prediction in CASP13
Y Li, C Zhang, EW Bell, DJ Yu, Y Zhang
Proteins: Structure, Function, and Bioinformatics, 2019
1042019
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
812021
Predicting protein-DNA binding residues by weightedly combining sequence-based features and boosting multiple SVMs
J Hu, Y Li, M Zhang, X Yang, HB Shen, DJ Yu
IEEE/ACM transactions on computational biology and bioinformatics 14 (6 …, 2016
772016
ATPbind: accurate protein–ATP binding site prediction by combining sequence-profiling and structure-based comparisons
J Hu, Y Li, Y Zhang, DJ Yu
Journal of chemical information and modeling 58 (2), 501-510, 2018
572018
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
562021
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
562021
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
502019
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
482020
TargetCrys: protein crystallization prediction by fusing multi-view features with two-layered SVM
J Hu, K Han, Y Li, JY Yang, HB Shen, DJ Yu
Amino acids 48, 2533-2547, 2016
402016
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
342022
GPCR–drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure
J Hu, Y Li, JY Yang, HB Shen, DJ Yu
Computational biology and chemistry 60, 59-71, 2016
292016
KNN-based dynamic query-driven sample rescaling strategy for class imbalance learning
J Hu, Y Li, WX Yan, JY Yang, HB Shen, DJ Yu
Neurocomputing 191, 363-373, 2016
272016
LOMETS3: Integrating deep learning and profile alignment for advanced protein template recognition and function annotation
W Zheng, Q Wuyun, X Zhou, Y Li, PL Freddolino, Y Zhang
Nucleic acids research 50 (W1), W454-W464, 2022
232022
Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14
Y Li, C Zhang, W Zheng, X Zhou, EW Bell, DJ Yu, Y Zhang
Proteins: Structure, Function, and Bioinformatics 89 (12), 1911-1921, 2021
222021
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