Related papers: SynCoGen: Synthesizable 3D Molecule Generation via…

We consider the conditional generation of 3D drug-like molecules with \textit{explicit control} over molecular properties such as drug-like properties (e.g., Quantitative Estimate of Druglikeness or Synthetic Accessibility score) and…

CAD programs, structured as parametric sequences of commands that compile into precise 3D geometries, are fundamental to accurate and efficient engineering design processes. Generating these programs from nonparametric data such as point…

Three-dimensional (3D) deep molecular generative models offer the advantage of goal-directed generation based on 3D-dependent properties, such as binding affinity for structure-based design within binding pockets. Traditional benchmarks…

Data-driven generative modeling has made remarkable progress by leveraging the power of deep neural networks. A reoccurring challenge is how to enable a model to generate a rich variety of samples from the entire target distribution, rather…

Predicting molecular conformations (or 3D structures) from molecular graphs is a fundamental problem in many applications. Most existing approaches are usually divided into two steps by first predicting the distances between atoms and then…

Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…

Crystal generative models have shown rapid progress for accelerating the discovery of bulk, periodic materials. However, many material systems such as 2D superconductors, thin film semiconductors, and catalytic surfaces are diperiodic,…

Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previous methods usually first predict the interatomic distances,…

Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…

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…

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

Molecular design and synthesis planning are two critical steps in the process of molecular discovery that we propose to formulate as a single shared task of conditional synthetic pathway generation. We report an amortized approach to…

The disconnect between AI-generated molecules with desirable properties and their synthetic feasibility remains a critical bottleneck in computational discovery of drugs and materials. While generative AI has accelerated the proposal of…

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…

Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a…

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular…

Function in natural systems arises from one-dimensional sequences forming three-dimensional structures with specific properties. However, current generative models suffer from critical limitations: training objectives seldom target function…

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…

The paradigm shift toward structure-driven molecule generation has been propelled by advances in deep generative models, such as variational auto-encoders and diffusion models. However, these generative models for molecular design remain…

3D generative models have shown significant promise in structure-based drug design (SBDD), particularly in discovering ligands tailored to specific target binding sites. Existing algorithms often focus primarily on ligand-target binding,…