Publications

jourals

• Xie et al. “CyclicBoltz1, fast and accurately predicting structures of cyclic peptides and complexes containing non-canonical amino acids using AlphaFold 3 Framework”Link for my paper, bioRxiv, 2025.

• Xie et al. “Antibody-SGM, a Score-Based Generative Model for Antibody Heavy-Chain Design”(link), Journal of Chemical Information and Modeling, 2024. Link for my paper

• Xie et al. “HelixDiff, a Score-Based Diffusion Model for Generating All-Atom α-Helical Structures”(link), ACS Central Science (IF 18.2), 2024. Link for my paper

• Xie et al. “HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures”(link), Bioinformatics 2023.Link for my paper

• Xie et al. “MHCherryPan, a novel pan-specific model for binding affinity prediction of class I HLA-peptide” (link), Int. J. Data Mining and Bioinformatics, Vol. 24, No. 3, 2020. Link for my paper

Conferences & workshops

• Xie et al. “HelixFlow, SE(3)–equivariant Full-atom Design of Peptides With Flow-matching Models”, Machine Learning for Structural Biology (MLSB) Workshop at NeurIPS 2024 .Link for my paper Link for my talk.

• Xie et al. “HelixDiff: Conditional Full-atom Design of Peptides With Diffusion Models”(link), Machine Learning for Structural Biology (MLSB) Workshop at NeurIPS 2023 Link for my paper

• Xie et al. “Antibody-SGM: Antigen-Specific Joint Design of Antibody Sequence and Structure using Diffusion Models”, Computational Biology Workshop at ICML 2023 Link for my paper

• Xie et al. “HelixGAN: A bidirectional Generative Adversarial Network with search in latent space for generation under constraints”(link), Machine Learning for Structural Biology (MLSB) Workshop at NeurIPS 2021. Link for my paper Link for my talk

• Xie, et al. “MHCherryPan, a novel model to predict the binding affinity of pan-specific class I HLA-peptide” (link), IEEE International Conference on Bioinformatics and Biomedicine (IEEE - BIBM) 2019. Link for my paper