Related papers: Structure-based drug design by denoising voxel gri…

Molecular structure elucidation from spectra is a fundamental challenge in molecular science. Conventional approaches rely heavily on expert interpretation and lack scalability, while retrieval-based machine learning approaches remain…

Proteins in complex with small molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. We here present a graph-based…

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…

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…

The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restricted to single-domain molecules, failing to address…

Structure-based virtual screening (SBVS) is a key workflow in computational drug discovery. SBVS models are assessed by measuring the enrichment of known active molecules over decoys in retrospective screens. However, the standard formula…

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…

Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds are computationally screened, de novo drug design based on the…

The ability to rapidly develop materials with desired properties has a transformative impact on a broad range of emerging technologies. In this work, we introduce a new framework based on the diffusion model, a recent generative machine…

We present a novel method for characterizing the microstructure of a material from volumetric datasets such as 3D image data from computed tomography (CT). The method is based on a new statistical model for the distribution of voxel…

While score based generative models, or diffusion models, have found success in image synthesis, they are often coupled with text data or image label to be able to manipulate and conditionally generate images. Even though manipulation of…

Generative AI has made rapid progress in text, image, and video synthesis, yet text-to-3D modeling for scientific design remains particularly challenging due to limited controllability and high computational cost. Most existing 3D…

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…

Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learning methods, from early regression models to recent…

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering.…

Recent advances in generative deep learning have transformed small molecule design, but most methods lack biological systems context, focusing narrowly on specific protein pockets. We introduce a non-differentiable diffusion guidance method…

We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are…

Structure-based drug design, i.e., finding molecules with high affinities to the target protein pocket, is one of the most critical tasks in drug discovery. Traditional solutions, like virtual screening, require exhaustively searching on a…

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), which aims to generate molecules that can bind tightly to the target protein, is an essential problem in drug discovery, and previous approaches have achieved initial success. However, most existing…