Zhengwei

Publications

1.Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Chunxiang Peng, Yiheng Zhu, Lydia Freddolino, Yang Zhang (2025) Single- and multi-domain protein structure prediction with D-I-TASSER. Nature Biotechnology, doi:10.1038/s41587-025-02654-4. 5-years IF=57.0 (first author)

2.Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, Lydia Freddolino, Yang Zhang. (2024) Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature Methods 21: 279–289. 5-years IF=45.6 (first author)

3.SM Mortuza, Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Yang Zhang (2021) Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications 12 (1), 5011. 5-years IF=16.1 (co-first author)

4.Pengshuo Yang#, Wei Zheng#, Kang Ning*, Yang Zhang*. (2021) Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. Proceedings of the National Academy of Sciences 118: e2110828118.5-years IF=10.8 (co-first author)

5.Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Lydia Freddolino, Yang Zhang. (2022) LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic Acids Research 50: W454-W464. 5-years IF=16.1 (first author)

6.Wei Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang (2019). LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acids Research, 47(W1), W429-W436. 5-years IF=16.1 (first author)

7.Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang (2020) FUpred: detecting protein domains through deep-learning-based contact map prediction. Bioinformatics, 36(12), 3749-3757. 5-years IF=7.6 (first author)

8.Chengxin Zhang, Wei Zheng, SM Mortuza, Yang Li, Yang Zhang (2020) DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics, 36(7), 2105-2112. 5-years IF=7.6(co-first author)

9.Wei Zheng, Qiqige Wuyun, Yang Zhang. (2024) One step forward towards deep-learning protein complex structure prediction by precise multiple sequence alignment construction. Clinical and Translational Medicine 14, no. 6. 5-years IF=8.0 (first author and co-corresponding author)

10.Wei Zheng, Qiqige Wuyun, Yang Li, SM Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, Yang Zhang (2019) Detecting distant-homology protein structures by aligning deep neural-network based contact maps. PLoS computational biology, 15(10), e1007411. 5-years IF=4.3 (first author)

11.Qiqige Wuyun, Wei Zheng, Zhenling Peng, Jianyi Yang (2018) A large-scale comparative assessment of methods for residue–residue contact prediction. Briefings in bioinformatics 19 (2), 219-230. 5-years IF=7.9 (co-first author)

12.Wei Zheng, Chengxin Zhang, Eric W Bell, Yang Zhang (2019) I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. Future Generation Computer Systems, 99, 73-85. 5-years IF=5.9 (first author)

13.Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W Bell, Yang Zhang (2021) Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods 1: 100014. 5-years IF=4.3 (first author)

14.Wei Zheng*, Qiqige Wuyun, Lydia Freddolino, Yang Zhang (2023). Integrating deep learning, threading alignments, and a multi‐MSA strategy for high‐quality protein monomer and complex structure prediction in CASP15. Proteins: Structure, Function, and Bioinformatics, 91 (12): 1684-1703. 5-yearsIF=2.8 (CASP15 invited paper, high cited paper，first author and corresponding author)

15.Wei Zheng, Yang Li, Chengxin Zhang, Xiaogen Zhou, Robin Pearce, Eric W Bell, Xiaoqiang Huang, Yang Zhang (2021). Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14. Proteins: Structure, Function, and Bioinformatics, 89: 1734-1751. 5-yearsIF=2.8 (CASP14 invited papaer, high cited paper，first author)

16.Wei Zheng, Yang Li, Chengxin Zhang, Robin Pearce, SM Mortuza, Yang Zhang (2019) Deep‐learning contact‐map guided protein structure prediction in CASP13. Proteins: Structure, Function, and Bioinformatics, 87(12), 1149-1164. 5-years IF=2.8 (CASP13 invited papaer, high cited paper，first author)

17.Wei Zheng, Qiqige Wuyun, Micah Cheng, Gang Hu, Yanping Zhang (2020) Two-level protein methylation prediction using structure model-based features. Scientific reports, 10(1), 6008. 5-years IF=4.3 (first author)

18.Chengxin Zhang, Wei Zheng, Micah Cheng, Gilbert S Omenn, Peter L Freddolino, Yang Zhang (2021) Functions of essential genes and a scale-free protein interaction network revealed by structure-based function and interaction prediction for a minimal genome. Journal of proteome research, 20(2), 1178-1189. 5-years IF=4.1 (co-first author)

19.Chenyue Zhang, Qinxin Wang, Yiyang Li, Anqi Teng, Gang Hu, Qiqige Wuyun, Wei Zheng (2024). The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction.Biomolecules,14 (12), 1531. 5-years IF=5.4 (corresponding author)

20.Qiqige Wuyun, Yihan Chen, Yifeng Shen, Yang Cao, Gang Hu, Wei Cui, Jianzhao Gao, Wei Zheng. (2024) Recent progress of protein tertiary structure prediction. Molecules 29 (4), 832. 5-yearsIF=4.6 (corresponding author)

21.Wei Zheng, Chen Zhang, Michelle Hanlon, Jishou Ruan, Jianzhao Gao (2014) An ensemble method for prediction of conformational B-cell epitopes from antigen sequences. Computational biology and chemistry 49, 51-58. 5-years IF=2.6 (first author)

22.Wei Zheng, Jishou Ruan, Gang Hu, Kui Wang, Michelle Hanlon, Jianzhao Gao (2015) Analysis of conformational B-cell epitopes in the antibody-antigen complex using the depth function and the convex hull. PloS one 10 (8), e0134835. 5-years IF=3.3 (first author)

23.Stephanie Tseng-Rogenski, Wei Zheng, Minoru Koi, Yang Zhang, John M Carethers (2019) 455–Differential Post-Translational Modification of Polymorphic Msh3 and Novel Binding Partner Nemo is Associated with Its Nuclear-To-Cytosol Shuttling. Gastroenterology, 156(6), S-96. 5-years IF=25.4

24.Xiaogen Zhou, Wei Zheng, Yang Li, Robin Pearce, Chengxin Zhang, Eric W Bell, Guijun Zhang, Yang Zhang. (2022) I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction. Nature Protocols 17: 2326-2353. 5-years IF=17.5

25.Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang. (2022) Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nature Computational Science 2: 265-275. 5-years IF=12.1

26.Haifeng Zhang, Renjie Shang, Kwantae Kim, Wei Zheng, Christopher J Johnson, Lei Sun, Xiang Niu, Liang Liu, et al. (2022) Evolution of a chordate-specific mechanism for myoblast fusion. Science Advances 8: eadd2696. 5-years IF=13.8

27.Young-Tae Lee, Alex Ayoub, Sang-Ho Park, Liang Sha, Jing Xu, Fengbiao Mao, Wei Zheng, Yang Zhang, Uhn-Soo Cho, Yali Dou (2021) Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin. Nature Communications 12 (1), 2953. 5-years IF=16.1

28.Sang Ho Park, Alex Ayoub, Young-Tae Lee, Jing Xu, Hanseong Kim, Wei Zheng, Biao Zhang, Liang Sha, Sojin An, Yang Zhang, Michael A Cianfrocco, Min Su, Yali Dou, Uhn-Soo Cho (2019) Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Nature Communications, 10(1), 5540. 5-years IF=16.1

29.Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang. (2022) DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Research 50: W235-W245.  5-years IF=16.1

30.Jaie Woodard, Wei Zheng, Yang Zhang. (2021) Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. PLoS computational biology, 17 (9), e1009370. 5-yearsIF=4.3

31.Xiaoqiang Huang, Wei Zheng, Robin Pearce, Yang Zhang (2020) SSIPe: accurately estimating protein–protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics, 36(8), 2429-2437. 5-years IF=7.6

32.Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W Bell, Xiaogen Zhou, Yang Zhang (2020) 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. Journal of proteome research, 19(4), 1351-1360. 5-years IF=4.1

33.Chengxin Zhang, Wei Zheng, Peter L Freddolino, Yang Zhang (2018) MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein–protein network mapping. Journal of molecular biology, 430(15), 2256-2265. 5-years IF=4.9

34.Ziying Zhang, Yaxian Cai, Biao Zhang, Wei Zheng, Lydia Freddolino, Guijun Zhang, Xiaogen Zhou. (2024) EM2:assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. Briefings in Bioinformatics, 25 (2), bbae113. 5-yearsIF=7.9

35.Brinda Vallat, Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin M Webb, Augustin Žídek, Wei Zheng, Ezra Peisach, Dennis W Piehl, et al. (2023) ModelCIF: an extension of PDBx/mmCIF data representation for computed structure models. Journal of molecular biology, 435 (14), 168021. 5-yearsIF=4.9

36.Mariantonietta Di Stefano, Giuseppina Faleo, Thomas Leitner, Wei Zheng, Yang Zhang, Amna Hassan, Marwan J Alwazzeh, Josè R Fiore, Mona Ismail, Teresa A Santantonio. (2023) Molecular and genetic characterization of hepatitis B virus (HBV) among Saudi chronically HBV-infected individuals. Viruses, 15 (2), 458. 5-yearsIF=4.0

37.M Paula Goetting-Minesky, Valentina Godovikova, Wei Zheng, J Christopher Fenno. (2022) Characterization of Treponema denticola major surface protein (Msp) by deletion analysis and advanced molecular modeling. Journal of Bacteriology, 204 (9), e00228-22. 5-yearsIF=3.0

38.Yang Li, Chengxin Zhang, Wei Zheng, Xiaogen Zhou, Eric W Bell, Dong‐Jun Yu, Yang Zhang. (2021) Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. Proteins: Structure, Function, and Bioinformatics, 89 (12), 1911-1921. 5-yearsIF=2.8

39.Siqi Wu, Chang Tian, Panpan Liu, Dongjie Guo, Wei Zheng, Xiaoqiang Huang, Yang Zhang, Lijun Liu (2021) Effects of SARS‐CoV‐2 mutations on protein structures and intraviral protein–protein interactions. Journal of medical virology, 93(4), 2132-2140. 5-years IF=6.6

40.Yang Li, Chengxin Zhang, Eric W Bell, Wei Zheng, Xiaogen Zhou, Dong-Jun Yu, Yang Zhang (2021) Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS computational biology, 17(3), e1008865. 5-years IF=4.3

41.Zhui Tu, Xiaoqiang Huang, Jinheng Fu, Na Hu, Wei Zheng, Yanping Li, Yang Zhang (2020) Landscape of variable domain of heavy‐chain‐only antibody repertoire from alpaca. Immunology, 161(1), 53-65. 5-years IF=6.6

42.Stephanie S Tseng-Rogenski, Koji Munakata, Daniel Y Choi, Paul K Martin, Supal Mehta, Minoru Koi, Wei Zheng, Yang Zhang, John M Carethers (2020) The human DNA mismatch repair protein MSH3 contains nuclear localization and export signals that enable nuclear-cytosolic shuttling in response to inflammation. Molecular and cellular biology, 40(13), e00029-20. 5-years IF=4.1

43.Yang Li, Wei Zheng, Qiqige Wuyun, Shujuan Cao, Jishou Ruan, Yanping Zhang (2018) A Novel Method for Drug Screen to Regulate G Protein‐Coupled Receptors in the Metabolic Network of Alzheimer’s Disease. BioMed Research International 2018 (1), 5486403. 5-years IF=3.1

44.Tong Wang, Wei Zheng, Qiqige Wuyun, Zhenfeng Wu, Jishou Ruan, Gang Hu, Jianzhao Gao (2017) PrAS: Prediction of amidation sites using multiple feature extraction. Computational biology and chemistry 66, 57-62. 5-years IF=2.6

45.Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang (2017) BindProfX: assessing mutation-induced binding affinity change by protein interface profiles with pseudo-counts. Journal of molecular biology 429 (3), 426-434. 5-years IF=4.9

46.Qiqige Wuyun, Wei Zheng, Yanping Zhang, Jishou Ruan, Gang Hu (2016) Improved species-specific lysine acetylation site prediction based on a large variety of features set. PloS one 11 (5), e0155370. 5-years IF=3.3

47.Yanping Zhang, Wei Zheng, Shuyi Liu, Chunguang Zhao (2016) gDNA-Prot: Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of protein sequence. Journal of Theoretical Biology 406, 8-16. 5-years IF=1.9

48.Yanping Zhang, Yajun Sheng, Wei Zheng, Pingan He, Jishuo Ruan (2015) Novel numerical characterization of protein sequences based on individual amino acid and its application. BioMed research international 2015 (1), 909567. 5-years IF=3.1

49.Weijun Ma, Chaofeng Yuan, Haidong Liu, Wei Zheng, Ying Zhou (2015) Genome-wide interaction analysis of quantitative traits in outbred mice. Genetics Research 97, e9. 5-years IF=1.5

50.Yanping Zhang, Jun Xu, Wei Zheng, Chen Zhang, Xingye Qiu, Ke Chen, Jishou Ruan (2014) newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation. Computational biology and chemistry 52, 51-59. 5-years IF=2.6

51.Yajun Sheng, Xingye Qiu, Chen Zhang, Jun Xu, Yanping Zhang, Wei Zheng, Ke Chen (2014) Quad‐PRE: A Hybrid Method to Predict Protein Quaternary Structure Attributes. Computational and mathematical methods in medicine 2014 (1), 715494. 5-years IF=2.8

52.Yajun Sheng, Chen Zhang, Xingye Qiu, Wei Zheng, Jishou Ruan, Yiming Shao (2013) Exploring the molecular mechanism of action between drug and RNA polymerase based on partially-resolved spatial structures. Current Computer-Aided Drug Design 9 (4), 547-555. 5-years IF=1.5