Related papers: Apo2Mol: 3D Molecule Generation via Dynamic Pocket…

Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change…

Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem…

The integration of deep learning, particularly AI-Generated Content, with high-quality data derived from ab initio calculations has emerged as a promising avenue for transforming the landscape of scientific research. However, the challenge…

Deep generative models for structure-based drug design (SBDD), where molecule generation is conditioned on a 3D protein pocket, have received considerable interest in recent years. These methods offer the promise of higher-quality molecule…

Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…

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…

Can we train a 3D molecule generator using data from dense regions to generate samples in sparse regions? This challenge can be framed as an out-of-distribution (OOD) generation problem. While prior research on OOD generation predominantly…

Molecular docking is a cornerstone of drug discovery, relying on high-resolution ligand-bound structures to achieve accurate predictions. However, obtaining these structures is often costly and time-intensive, limiting their availability.…

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…

Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free…

To design a drug given a biological molecule by using deep learning methods, there are many successful models published recently. People commonly used generative models to design new molecules given certain protein. LiGAN was regarded as…

Generative AI presents chemists with novel ideas for drug design and facilitates the exploration of vast chemical spaces. Diffusion models (DMs), an emerging tool, have recently attracted great attention in drug R\&D. This paper…

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…

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…

We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new representation of protein structure, relies on a novel…

Generative models of 3D molecular structure play a rapidly growing role in the design and simulation of molecules. Diffusion models currently dominate the space of 3D molecule generation, while autoregressive models have trailed behind. In…

Generating chemically valid 3D molecular conformations is critical for computational drug discovery. Classical diffusion-based models like GeoLDM perform well but require hundreds of steps, making large-scale in silico screening…

Recently, deep generative models for molecular graphs are gaining more and more attention in the field of de novo drug design. A variety of models have been developed to generate topological structures of drug-like molecules, but…

De novo molecular design has facilitated the exploration of large chemical space to accelerate drug discovery. Structure-based de novo method can overcome the data scarcity of active ligands by incorporating drug-target interaction into…

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as…