Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression. - Dong-Jun Yu; Yang Li 107; Jun Hu 011; Xibei Yang; Jing-Yu Yang 001; Hong-Bin Shen (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

GPCR-drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure. - Jun Hu 011; Yang Li 107; Jing-Yu Yang 001; Hong-Bin Shen; Dong-Jun Yu (Comput. Biol. Chem., 2016)

KNN-based dynamic query-driven sample rescaling strategy for class imbalance learning. - Jun Hu 011; Yang Li 107; Wuxia Yan; Jing-Yu Yang 001; Hong-Bin Shen; Dong-Jun Yu (Neurocomputing, 2016)

Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs. - Jun Hu 011; Yang Li 107; Ming Zhang 033; Xibei Yang; Hong-Bin Shen; Dong-Jun Yu (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. - Jun Hu 011; Yang Li 107; Yang Zhang 040; Dong-Jun Yu (J. Chem. Inf. Model., 2018)

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. - Yang Li 107; Jun Hu 011; Chengxin Zhang; Dong-Jun Yu; Yang Zhang 040 (Bioinform., 2019)

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. - Wei Zheng 013; Chengxin Zhang; Qiqige Wuyun; Robin Pearce; Yang Li 107; Yang Zhang 040 (Nucleic Acids Res., 2019)

Detecting distant-homology protein structures by aligning deep neural-network based contact maps. - Wei Zheng 013; Qiqige Wuyun; Yang Li 107; S. M. Mortuza; Chengxin Zhang; Robin Pearce; Jishou Ruan; Yang Zhang 040 (PLoS Comput. Biol., 2019)

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. - Chengxin Zhang; Wei Zheng 013; S. M. Mortuza; Yang Li 107; Yang Zhang 040 (Bioinform., 2020)

FUpred: detecting protein domains through deep-learning-based contact map prediction. - Wei Zheng 013; Xiaogen Zhou; Qiqige Wuyun; Robin Pearce; Yang Li 107; Yang Zhang 040 (Bioinform., 2020)

SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network. - Ming-Cai Chen; Yang Li 107; Yi-Heng Zhu 001; Fang Ge; Dong-Jun Yu (J. Chem. Inf. Model., 2020)

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. - Yang Li 107; Chengxin Zhang; Eric W. Bell; Wei Zheng 013; Xiaogen Zhou; Dong-Jun Yu; Yang Zhang 040 (PLoS Comput. Biol., 2021)

LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. - Wei Zheng 013; Qiqige Wuyun; Xiaogen Zhou; Yang Li 107; Peter L. Freddolino; Yang Zhang 040 (Nucleic Acids Res., 2022)

DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. - Xiaogen Zhou; Chunxiang Peng; Wei Zheng 013; Yang Li 107; Guijun Zhang; Yang Zhang 040 (Nucleic Acids Res., 2022)

Progressive assembly of multi-domain protein structures from cryo-EM density maps. - Xiaogen Zhou; Yang Li 107; Chengxin Zhang; Wei Zheng 013; Guijun Zhang; Yang Zhang 040 (Nat. Comput. Sci., 2022)

Fast and accurate Ab Initio Protein structure prediction using deep learning potentials. - Robin Pearce; Yang Li 107; Gilbert S. Omenn; Yang Zhang 040 (PLoS Comput. Biol., 2022)

MolMetaLM: a Physicochemical Knowledge-Guided Molecular Meta Language Model. - Yifan Wu; Min Zeng; Yang Li 107; Yang Zhang 040; Min Li (CoRR, 2024)

Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction". - Ivona Martinovic; Tin Vlasic; Yang Li 107; Bryan Hooi; Yang Zhang 040; Mile Sikic (Zenodo, 2024)

Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction". - Ivona Martinovic; Tin Vlasic; Yang Li 107; Bryan Hooi; Yang Zhang 040; Mile Sikic (Zenodo, 2024)