Related papers: Chem3DLLM: 3D Multimodal Large Language Models for…

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language…

Structure-based drug design (SBDD) is crucial for developing specific and effective therapeutics against protein targets but remains challenging due to complex protein-ligand interactions and vast chemical space. Although language models…

Large Language Models demonstrate substantial promise for advancing scientific discovery, yet their deployment in disciplines demanding factual precision and specialized domain constraints presents significant challenges. Within molecular…

Accurately predicting 3D structures and dynamics of physical systems is crucial in scientific applications. Existing approaches that rely on geometric Graph Neural Networks (GNNs) effectively enforce $\mathrm{E}(3)$-equivariance, but they…

Large Language Models (LLMs) have significantly advanced molecular discovery, but existing multimodal molecular architectures fundamentally rely on autoregressive (AR) backbones. This strict left-to-right inductive bias is sub-optimal for…

Recent developments in Multimodal Large Language Models (MLLMs) have significantly improved Vision-Language (VL) reasoning in 2D domains. However, extending these capabilities to 3D scene understanding remains a major challenge. Existing 3D…

Generating precise 3D molecular geometries is crucial for drug discovery and material science. While prior efforts leverage 1D representations like SELFIES to ensure molecular validity, they fail to fully exploit the rich chemical knowledge…

Large Language Models (LLMs) have made great strides in areas such as language processing and computer vision. Despite the emergence of diverse techniques to improve few-shot learning capacity, current LLMs fall short in handling the…

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal…

Structure-based drug design aims at generating high affinity ligands with prior knowledge of 3D target structures. Existing methods either use conditional generative model to learn the distribution of 3D ligands given target binding sites,…

Multimodal scientific reasoning remains a significant challenge for large language models (LLMs), particularly in chemistry, where problem-solving relies on symbolic diagrams, molecular structures, and structured visual data. Here, we…

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…

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D)…

The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to…

Structure-Based Drug Design (SBDD) has revolutionized drug discovery by enabling the rational design of molecules for specific protein targets. Despite significant advancements in improving docking scores, advanced 3D-SBDD generative models…

Unlike vision and language data which usually has a unique format, molecules can naturally be characterized using different chemical formulations. One can view a molecule as a 2D graph or define it as a collection of atoms located in a 3D…

Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges:…

Large language models (LLMs) have demonstrated broad utility across molecular domains, spanning drug discovery and materials design. Analyzing LLMs' latent representations is crucial for elucidating their underlying mechanisms, improving…

This paper presents ShapeLLM, the first 3D Multimodal Large Language Model (LLM) designed for embodied interaction, exploring a universal 3D object understanding with 3D point clouds and languages. ShapeLLM is built upon an improved 3D…

Pretraining molecular representations is crucial for drug and material discovery. Recent methods focus on learning representations from geometric structures, effectively capturing 3D position information. Yet, they overlook the rich…