14 accepted papers
Recent advances in $\textit{de novo}$ protein binder design have enabled increasing experimental validation, yet reported $\textit{in silico}$ metrics remain difficult to interpret or compare across studies due to non-standardized evaluation protocols. We introduce $\textbf{ProtDBench}$, a standardi…
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…
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 generative models have shown great promise in peptide generation. However, several challenges remain in designing effective pepti…
The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with rigid structures, limiting their practical application in d…
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…
Designing 3D ligands within a target binding site is a fundamental task in drug discovery. Existing structured-based drug design methods treat all ligand atoms equally, which ignores different roles of atoms in the ligand for drug design and can be less efficient for exploring the large drug-like mo…
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…
This paper studies an important problem in computational chemistry: predicting a molecule's spatial atom arrangements, or a molecular conformation. We propose a neural energy minimization formulation that casts the prediction problem into an unrolled optimization process, where a neural network is p…
Equivariance has been a long-standing concern in various fields ranging from computer vision to physical modeling. Most previous methods struggle with generality, simplicity, and expressiveness --- some are designed ad hoc for specific data types, some are too complex to be accessible, and some sacr…
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…
We study a fundamental problem in structure-based drug design --- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are mostly string-based or graph-based. They are limited by the…
Automatically reasoning about future human behaviors is a difficult problem but has significant practical applications to assistive systems. Part of this difficulty stems from learning systems' inability to represent all kinds of behaviors. Some behaviors, such as motion, are best described with con…