5 papers
Scalable Peptide Design via Memory-Efficient Equivariant Transformer
Rui Jiao, Xiangzhe Kong, Yinjun Jia +4
Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints. Latent generative frameworks offer an effective route for this probl…
Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding
Xinheng He, Yijia Zhang, Haowei Lin +4
Structure-based drug design has seen significant advancements with the integration of artificial intelligence (AI), particularly in the generation of hit and lead compounds. Howeve…
Assay2Mol: large language model-based drug design using BioAssay context
Yifan Deng, Spencer S. Ericksen, Anthony Gitter
Scientific databases aggregate vast amounts of quantitative data alongside descriptive text. In biochemistry, molecule screening assays evaluate candidate molecules' functional res…
Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints
Dapeng Jiang, Xiangzhe Kong, Jiaqi Han +6
Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical need…
UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design
Xiangzhe Kong, Zishen Zhang, Ziting Zhang +5
The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restr…