7 papers
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…
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
Xingang Peng, Shitong Luo, Jiaqi Guan +3
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the spe…
Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension
Jiahan Li, Tong Chen, Shitong Luo +7
Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generativ…
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
Xiangxin Zhou, Yi Xiao, Haowei Lin +7
The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug…
Orientation-Aware Graph Neural Networks for Protein Structure Representation Learning
Jiahan Li, Shitong Luo, Congyue Deng +5
By folding into particular 3D structures, proteins play a key role in living beings. To learn meaningful representation from a protein structure for downstream tasks, not only the…
Group Ligands Docking to Protein Pockets
Jiaqi Guan, Jiahan Li, Xiangxin Zhou +5
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, t…