11 accepted papers
Generative modeling of three-dimensional (3D) molecules is a fundamental yet challenging problem in drug discovery and materials science. Existing approaches typically represent molecules as 3D graphs and co-generate discrete atom types with continuous atomic coordinates, leading to intrinsic learni…
Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in conditional scenarios where specific molecular properties must be…
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, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding…
Dual-target therapeutic strategies have become a compelling approach and attracted significant attention due to various benefits, such as their potential in overcoming drug resistance in cancer therapy. Considering the tremendous success that deep generative models have achieved in structure-based d…
Rich data and powerful machine learning models allow us to design drugs for a specific protein target <em>in silico</em>. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free models as the atomic interaction in the 3D space is explicitl…
Message Passing Neural Networks (MPNNs) are a widely used class of Graph Neural Networks (GNNs). The limited representational power of MPNNs inspires the study of provably powerful GNN architectures. However, knowing one model is more powerful than another gives little insight about what functions t…
Targeted protein degradation techniques, such as PROteolysis TArgeting Chimeras (PROTACs), have emerged as powerful tools for selectively removing disease-causing proteins. One challenging problem in this field is designing a linker to connect different molecular fragments to form a stable drug-cand…
Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding bond solution for the temporally generated at…
Deep learning has achieved tremendous success in designing novel chemical compounds with desirable pharmaceutical properties. In this work, we focus on a new type of drug design problem — generating a small “linker” to physically attach two independent molecules with their distinct functions. The ma…
Antibodies are immune system proteins that protect the host by binding to specific antigens such as viruses and bacteria. The binding between antibodies and antigens is mainly determined by the complementarity-determining regions (CDR) of the antibodies. In this work, we develop a deep generative mo…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown potential in advancing the specificity and success rate of in silico drug design by considering the structure of protein pockets. This setting posts fundamental…