Related papers: Benchmarking structure-based three-dimensional mol…

The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with…

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding…

Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold relationship, as well as the difficulties to capture the…

Rapid advancements in text-to-3D generation require robust and scalable evaluation metrics that align closely with human judgment, a need unmet by current metrics such as PSNR and CLIP, which require ground-truth data or focus only on…

Structure-based drug design has seen significant advancements with the integration of artificial intelligence (AI), particularly in the generation of hit and lead compounds. However, most AI-driven approaches neglect the importance of…

AI-assisted coding has rapidly reshaped software practice and research workflows, yet today's models still struggle to produce correct code for complex 3D geometric vision. If models could reliably write such code, the research of our…

Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying…

A pharmacophore consists of the parts of the structure of the ligand that are sufficient to express the biological and pharmacological effects of the ligand. It is usually a substructure of the entire structure of the ligand. Small organic…

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…

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…

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the…

Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to…

Structure-based drug design (SBDD) faces a fundamental scaling fidelity dilemma: rich pocket-aware conditioning captures interaction geometry but can be costly, often scales quadratically ($O(L^2)$) or worse with protein length ($L$), while…

We propose MVGBench, a comprehensive benchmark for multi-view image generation models (MVGs) that evaluates 3D consistency in geometry and texture, image quality, and semantics (using vision language models). Recently, MVGs have been the…

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…

Molecular similarity plays a central role in ligand-based drug discovery, such as virtual screening, analog searching, and goal-directed molecular generation. However, traditional similarity measures, ranging from fingerprint-based Tanimoto…

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)…

World Generation Models are emerging as a cornerstone of next-generation multimodal intelligence systems. Unlike traditional 2D visual generation, World Models aim to construct realistic, dynamic, and physically consistent 3D/4D worlds from…

Fast generation of high-quality 3D digital humans is important to a vast number of applications ranging from entertainment to professional concerns. Recent advances in differentiable rendering have enabled the training of 3D generative…

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…