RESEARCH INTERESTS

  • Computer aided drug design
  • Protein design and redesign
  • Antibody engineering

招生（生信、生物、计算机、药学等专业背景均可）：

  • 计算机辅助药物设计算法开发与实验研究
  • 蛋白设计的算法与实验研究

CONTACT US

  • Yang Cao, PhD
  • School of Life Sciences
  • Sichuan University
  • Chengdu, China
  • Email: cy_scu.AT.yeah.net (please replace .AT. with @)

PUBLICATIONS

  • L Zhang, W Song, T Zhu, Y Liu, W Chen, Y Cao*.ConvNeXt-MHC: Improving MHC peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model. Briefings in Bioinformatics. accept. 2024.
  • Y Wang, Y Yang, Y Liu, ZX Xiao, Yang Cao*. FitDockApp: a Graphical User Interface Plugin for Template-based Docking With PyMOL. Progress in Biochemistry and Biophysics. 51(3):716-725, 2024.
  • Q Wuyun, Y Chen, Y Shen, Y Cao*, G Hu*, W Cui*, J Gao*, W Zheng*. Recent Progress of Protein Tertiary Structure Prediction. Molecules . 29 (4), 832, 2024.
  • J Wei, J Li, F Zong, ZX Xiao, Y Cao*. Current Protocols. 4(2), e1002, 2024.
  • F Zong, C Long, W Hu, S Chen, W Dai, ZX Xiao, Y Cao*. Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. Nucleic Acids Research. 51 (W1), W17-W24, 2023.
  • Y Liu, Y Cao*. Protein–Ligand Blind Docking Using CB-Dock2. Computational Drug Discovery and Design. 113-125, 2023.
  • J Wang, Y Cao, B Lai, Y Liu, C Li, C Bu. Discovery selective acetylcholinesterase inhibitors to control Tetranychus urticae (Acari: Tetranychidae). Journal of Insect Science. 23 (4), 19, 2023.
  • J Gan, J Liu, Y Liu, S Chen, W Dai, ZX Xiao, Y Cao*. DrugRep: an automatic virtual screening server for drug repurposing. Acta Pharmacologica Sinica. 44 (4), 888-896; 2023
  • Y Liu, X Yang, J Gan, S Chen, ZX Xiao, Y Cao*. CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Research. 50(W1), W159–W164, 2022.
  • L Li#, M Gao#, P Jiao#, S Zu#, Y Deng#, D Wan#, Y Cao#, J Duan, SR Aliyari, J Li, ... Antibody engineering improves neutralization activity against K417 spike mutant SARS-CoV-2 variants. Cell & Bioscience 12 (1), 1-15, 2022
  • X Yang, Y Liu, J Gan, ZX Xiao, Y Cao*. FitDock: protein–ligand docking by template fitting. Briefings in Bioinformatics. 23 (3), bbac087, 2022
  • Y Liu, J Gan, R Wang, X Yang, Z Xiao, Y Cao*. DrugDevCovid19: An Atlas of Anti-COVID-19 Compounds Derived by Computer-Aided Drug Design. Molecules. 27 (3), 683, 2022.
  • R Luo, B Qu, L An, Y Zhao, Y Cao*, P Ren*, H Hang*. Simultaneous Maturation of Single Chain Antibody Stability and Affinity by CHO Cell Display. Bioengineering 9 (8), 360. 2022
  • M Niu , J Xu , Y Liu , Y Li , T He , L Ding , Y He , Y Yi , F Li , R Guo , Y Gao , R Li , L Li , M Fu , Q Hu , Y Luo , C Zhang , K Qin , J Yi , S Yu , J Yang , H Chen , L Wang , Z Li , B Dong , S Qi , L Ouyang , Y Zhang , Y Cao*, ZX Xiao*. FBXL2 counteracts Grp94 to destabilize EGFR and inhibit EGFR-driven NSCLC growth. Nature Communications. 12，1-15, 2021
  • L Song, D Cohen, Z Ouyang, Y Cao, X Hu, XS Liu*. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nature Methods. 18，627-630, 2021
  • A Wu#, L Wang#, H Zhou#, C Ji, S Xia, Y Cao, J Meng, X Ding, S Gold, T Jiang*, G Cheng*. One year of SARS-CoV-2 evolution. CELL HOST & MICROBE. 29, 503-507, 2021
  • R Fu, P Zhang, G Jin, L Wang, S Qi, Y Cao, C Martin, Y Zhang*. Versatility in acyltransferase activity completes chicoric acid biosynthesis in purple coneflower. Nature communications. 29, 503-507, 2021
  • J Nie#, Q Li#, L Zhang#, Y Cao#, Y Zhang, T Li, J Wu, S Liu, M Zhang, C Zhao, ... Functional comparison of SARS-CoV-2 with closely related pangolin and bat coronaviruses. Cell discovery 7 (1), 1-12, 2021
  • C Li#, Y Cao#, J Yang, M Li, B Li, C Bu. Acetylcholinesterase target sites for developing environmentally friendly insecticides against Tetranychus urticae (Acari: Tetranychidae). Experimental and Applied Acarology, 1-13, 2021
  • M Grimm, Y Liu, X Yang, C Bu, ZX Xiao, and Y Cao*. LigMate: A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening. Journal of Chemical Information and Modeling. (Online, DOI: 10.1021/acs.jcim.9b01210), 2020
  • Y Liu#, H He#, ZX Xiao, A Ji, J Ye, Q Sun*, Y Cao*. A systematic analysis of miRNA markers and classification algorithms for forensic body fluid identification. Briefings in Bioinformatics. (Online, DOI: 10.1093/bib/bbaa324), 2020
  • Y Liu#, M Grimm#, W Dai, M Hou, ZX Xiao, Y Cao*. CB-Dock: a web server for cavity detection-guided protein-ligand blind docking. Acta Pharmacologica Sinica. 41 (1), 138-144, 2020
  • L Li#, S Chen#, Z Miao#, Y Liu, X Liu, ZX Xiao and Y Cao*. AbRSA: a Robust Tool for Antibody Numbering. Protein Science (https://doi.org/10.1002/pro.3633), 2019
  • Y Cao, W Dai, Z Miao. Evaluation of Protein-Ligand Docking by Cyscore. Methods in molecular biology 1762, 233-243, 2018
  • B Kong#, Y Cao#, D Wu, L An, F Ran, Y Lin, C Ye, H Wang*, H Hang*. Affinity maturation of an antibody for the UV-induced DNA lesions 6,4 pyrimidine-pyrimidones. Applied Microbiology and Biotechnology. 102(15) 6409-6424, 2018
  • C Li#, Z Wang#, Y Cao#, L Wang, J Ji, Z Chen, T Deng, T Jiang*, G Cheng*, F Qin*. Screening for Novel Small-Molecule Inhibitors Targeting the Assembly of Influenza Virus Polymerase Complex by a Bimolecular Luminescence Complementation-Based Reporter System. J Virol. 2017, 91(5): e02282-16.
  • Z Miao* and Y Cao*. Quantifying side-chain conformational variations in protein structure. Scientific Reports. 2016, 6: 37024
  • J Liu#, Z Miao#, L Li, ZX Xiao*, Yang Cao*. DRSP: a Structural Database for Single Residue Substitutions in PDB. Progress in Biochemistry and Biophysics. 2016, 43(8):810-816
  • J Guo#, Y Cao#, K Qin, X Zhao, D Wang, Z Li, L Xin,Y Shu, J Zhou*. Limited effect of recombinant human mannose-binding lectin on the infection of novel influenza A (H7N9) virus in vitro. Biochem Biophys Res Commun. 2015, 458(1):77-81
  • Y Cao*, L Li., Improved protein-ligand binding affinity prediction by using a curvature dependent surface area model, Bioinformatics, 30(12):1674-1680, 2014
  • L Huang#, Y Cao#, J Zhou, K Qin, W Zhu, Y Zhu, L Yang, D Wang, H Wei*, Y Shu*., A conformational restriction in influenza A virus neuraminidase binding site by R152 caused the combinational effect of I222T with H274Y on oseltamivir resistance. Antimicrob Agents Chemother. 58(3), 1639-1645, 2014
  • Z Miao, Y Cao, T Jiang. Modeling of protein side-chain conformations with RASP, Protein Structure Prediction, 3rd Edition (Methods in Molecular Biology), Springer, 2014
  • AM Larson, H Wang, Y Cao, T Jiang, J Chen, AM Klibanov*., Conjugating drug candidates to polymeric chains does not necessarily enhance anti-influenza activity., J Pharm Sci., 101(10), 3896-905, 2012
  • Y Cao, L Song, Z Miao, Y Hu, L Tian, T Jiang*., Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation, Bioinformatics, 27(6), 785-790,2011
  • Y Cao, X Koh, L Dong, X Du, A Wu, X Ding, H Deng, Y Shu*, J Chen*, T Jiang*., Rapid Estimation of Binding Activity of Influenza Virus Hemagglutinin to Human and Avian Receptors, PLoS One, 6(4):e18664, 2011
  • Z Miao Z, Y Cao, T Jiang., RASP: rapid modeling of protein side chain conformations, Bioinformatics, 27(22), 3117-22, 2011