Related papers: Applications of Modular Co-Design for De Novo 3D M…

Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D \textit{de novo} generation), has become a fundamental task in drug designs. Existing diffusion-based 3D molecule generation methods could suffer from…

In the field of computational molecule generation, an essential task in the discovery of new chemical compounds, fragment-based deep generative models are a leading approach, consistently achieving state-of-the-art results in molecular…

Diffusion models have emerged as powerful tools for molecular generation, particularly in the context of 3D molecular structures. Inspired by non-equilibrium statistical physics, these models can generate 3D molecular structures with…

Equivariant diffusion models have achieved impressive performance in 3D molecule generation. These models incorporate Euclidean symmetries of 3D molecules by utilizing an SE(3)-equivariant denoising network. However, specialized equivariant…

Structure-based drug design involves finding ligand molecules that exhibit structural and chemical complementarity to protein pockets. Deep generative methods have shown promise in proposing novel molecules from scratch (de-novo design),…

Finding drug-like compounds with high bioactivity is essential for drug discovery, but the task is complicated by the high cost of chemical synthesis and validation. With their outstanding performance in de novo drug design, deep generative…

Designing molecules with desirable physiochemical properties and functionalities is a long-standing challenge in chemistry, material science, and drug discovery. Recently, machine learning-based generative models have emerged as promising…

Shape-based virtual screening is widely employed in ligand-based drug design to search chemical libraries for molecules with similar 3D shapes yet novel 2D chemical structures compared to known ligands. 3D deep generative models have the…

Deep generative models that produce novel molecular structures have the potential to facilitate chemical discovery. Flow matching is a recently proposed generative modeling framework that has achieved impressive performance on a variety of…

Three-dimensional molecular structure generation is typically performed at the level of individual atoms, yet molecular graph generation techniques often consider fragments as their structural units. Building on the advances in frame-based…

A generative model capable of sampling realistic molecules with desired properties could accelerate chemical discovery across a wide range of applications. Toward this goal, significant effort has focused on developing models that jointly…

Deep generative models have been applied with increasing success to the generation of two dimensional molecules as SMILES strings and molecular graphs. In this work we describe for the first time a deep generative model that can generate 3D…

Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D for geometry-based conditional generation remains largely…

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 restricted to single-domain molecules, failing to address…

The idea of using deep-learning-based molecular generation to accelerate discovery of drug candidates has attracted extraordinary attention, and many deep generative models have been developed for automated drug design, termed molecular…

Machine learning has the potential to automate molecular design and drastically accelerate the discovery of new functional compounds. Towards this goal, generative models and reinforcement learning (RL) using string and graph…

Molecule generation is a very important practical problem, with uses in drug discovery and material design, and AI methods promise to provide useful solutions. However, existing methods for molecule generation focus either on 2D graph…

Recently, 3D generative models have shown promising performances in structure-based drug design by learning to generate ligands given target binding sites. However, only modeling the target-ligand distribution can hardly fulfill one of the…

Deep generative models that produce novel molecular structures have the potential to facilitate chemical discovery. Diffusion models currently achieve state of the art performance for 3D molecule generation. In this work, we explore the use…

Recent advances in generative models, particularly diffusion and auto-regressive models, have revolutionized fields like computer vision and natural language processing. However, their application to structure-based drug design (SBDD)…