newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation. - Yanping Zhang; Jun Xu 019; Wei Zheng 013; Chen Zhang; Xingye Qiu; Ke Chen 003; Jishou Ruan (Comput. Biol. Chem., 2014)

An ensemble method for prediction of conformational B-cell epitopes from antigen sequences. - Wei Zheng 013; Chen Zhang; Michelle Hanlon; Jishou Ruan; Jianzhao Gao (Comput. Biol. Chem., 2014)

Quad-PRE: A Hybrid Method to Predict Protein Quaternary Structure Attributes. - Yajun Sheng; Xingye Qiu; Chen Zhang; Jun Xu 019; Yanping Zhang; Wei Zheng 013; Ke Chen 003 (Comput. Math. Methods Medicine, 2014)

PrAS: Prediction of amidation sites using multiple feature extraction. - Tong Wang; Wei Zheng 013; Qiqige Wuyun; Zhenfeng Wu; Jishou Ruan; Gang Hu; Jianzhao Gao (Comput. Biol. Chem., 2017)

A large-scale comparative assessment of methods for residue-residue contact prediction. - Qiqige Wuyun; Wei Zheng 013; Zhenling Peng; Jianyi Yang 002 (Briefings Bioinform., 2018)

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. - Wei Zheng 013; Chengxin Zhang; Eric W. Bell; Yang Zhang 040 (Future Gener. Comput. Syst., 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)

SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. - Xiaoqiang Huang; Wei Zheng 013; Robin Pearce; Yang Zhang 040 (Bioinform., 2020)

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)

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)

Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. - Jaie C. Woodard; Wei Zheng 013; 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)

DMFold standalone package. - Wei Zheng 013 (Zenodo, 2023)

DeepMSA2 standalone package. - Wei Zheng 013 (Zenodo, 2023)

DMFold models for 5,042 human proteins. - Wei Zheng 013 (Zenodo, 2023)

DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. - Ziying Zhang; Yaxian Cai; Biao Zhang; Wei Zheng 013; Peter L. Freddolino; Guijun Zhang; Xiaogen Zhou (Briefings Bioinform., 2024)