Related papers: Target-aware Molecular Graph Generation

Structure-based drug design (SBDD), aiming to generate 3D molecules with high binding affinity toward target proteins, is a vital approach in novel drug discovery. Although recent generative models have shown great potential, they suffer…

Generating molecular graphs with desired chemical properties driven by deep graph generative models provides a very promising way to accelerate drug discovery process. Such graph generative models usually consist of two steps: learning…

Recent breakthroughs in generative modeling have demonstrated remarkable capabilities in molecular generation, yet the integration of comprehensive biomedical knowledge into these models has remained an untapped frontier. In this study, we…

Generating molecular graphs is crucial in drug design and discovery but remains challenging due to the complex interdependencies between nodes and edges. While diffusion models have demonstrated their potentiality in molecular graph design,…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Traditional drug discovery programs are being transformed by the advent of machine learning methods. Among these, Generative AI methods (GM) have gained attention due to their ability to design new molecules and enhance specific properties…

Methods for jointly generating molecular graphs along with their 3D conformations have gained prominence recently due to their potential impact on structure-based drug design. Current approaches, however, often suffer from very slow…

We propose an algorithm for learning a conditional generative model of a molecule given a target. Specifically, given a receptor molecule that one wishes to bind to, the conditional model generates candidate ligand molecules that may bind…

Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing…

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…

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,…

Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and…

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…

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…

Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine…

Graph-structured data jointly contain discrete topology and continuous geometry, which poses fundamental challenges for generative modeling due to heterogeneous distributions, incompatible noise dynamics, and the need for equivariant…

Molecular generation plays an important role in drug discovery and materials science, especially in data-scarce scenarios where traditional generative models often struggle to achieve satisfactory conditional generalization. To address this…

We propose a hierarchical normalizing flow model for generating molecular graphs. The model produces new molecular structures from a single-node graph by recursively splitting every node into two. All operations are invertible and can be…

Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the…