Sheng Chen

Education

• Ph.D in Computer Science, Sun Yat-sen University, 2021-2025 (expected)
• M.S. in Software Engineering, Sun Yat-sen University, 2018-2020
• B.S. in Software Engineering, Sun Yat-sen University, 2014-2018

Work experience

• 2022.8-2023.9: Director of AI
  • AIxplorerBio Inc.
  • Duties included: AI-enpowered dual-target drug design
  • Supervisor: David Daqiang Xu
• 2020.8-2021.5: Software Development Engineer
  • Huawei Technologies Co., Ltd.
  • Duties included: CI/CD tools development for HUAWEI Cloud
  • Supervisor: Yulin Zheng
• 2020.1-2020.5: AI Algorithm Intern
  • Baidu Inc.
  • Duties included: Vehicle damage assessment algorithm development
  • Supervisor: Wei Zhang

Publications

Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences

Chen, S., Zhang, S., Fang, X. et al. Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences. Nat Commun 15, 8808 (2024). https://doi.org/10.1038/s41467-024-53116-5

Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures

Song, Y., Yuan, Q., Chen, S., Zeng, Y., Zhao, H., & Yang, Y. (2024). Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures. Nature Communications, 15(1), 8180.

Structure-aware dual-target drug design through collaborative learning of pharmacophore combination and molecular simulation

Chen, S., Xie, J., Ye, R., Xu, D. D., & Yang, Y. (2024). Structure-aware dual-target drug design through collaborative learning of pharmacophore combination and molecular simulation. Chemical Science, 15(27), 10366-10380.

DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model

Xie, J., Chen, S., Lei, J., & Yang, Y. (2024). DiffDec: structure-aware scaffold decoration with an end-to-end diffusion model. Journal of Chemical Information and Modeling, 64(7), 2554-2564.

SE (3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation

Liu, D., Chen, S., Zheng, S., Zhang, S., & Yang, Y. (2023, December). SE (3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation. In 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 120-123). IEEE.

Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation

Wang, J., Chen, S., Yuan, Q., Chen, J., Li, D., Wang, L., & Yang, Y. (2024). Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. Journal of Computational Chemistry, 45(8), 436-445.

Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning

Yuan, Q., Chen, S., Wang, Y., Zhao, H., & Yang, Y. (2022). Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning. Briefings in bioinformatics, 23(6), bbac444.

AlphaFold2-aware protein–DNA binding site prediction using graph transformer

Yuan, Q., Chen, S., Rao, J., Zheng, S., Zhao, H., & Yang, Y. (2022). AlphaFold2-aware protein–DNA binding site prediction using graph transformer. Briefings in Bioinformatics, 23(2), bbab564.

SEGEM: A fast and accurate automated protein backbone structure modeling method for cryo-EM

Chen, S., Zhang, S., Li, X., Liu, Y., & Yang, Y. (2021, December). SEGEM: A fast and accurate automated protein backbone structure modeling method for cryo-EM. In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 24-31). IEEE.

Predicting drug–protein interaction using quasi-visual question answering system

Zheng, S., Li, Y., Chen, S., Xu, J., & Yang, Y. (2020). Predicting drug–protein interaction using quasi-visual question answering system. Nature Machine Intelligence, 2(2), 134-140.

To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map

Chen, S., Sun, Z., Lin, L., Liu, Z., Liu, X., Chong, Y., ... & Yang, Y. (2019). To improve protein sequence profile prediction through image captioning on pairwise residue distance map. Journal of chemical information and modeling, 60(1), 391-399.