Related papers: Geometric-informed GFlowNets for Structure-Based D…

DNA-encoded libraries (DELs) are a powerful approach for rapidly screening large numbers of diverse compounds. One of the key challenges in using DELs is library design, which involves choosing the building blocks that will be…

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target…

Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…

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…

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…

The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…

Designing ligand-binding proteins, such as enzymes and biosensors, is essential in bioengineering and protein biology. One critical step in this process involves designing protein pockets, the protein interface binding with the ligand.…

Point cloud semantic segmentation from projected views, such as range-view (RV) and bird's-eye-view (BEV), has been intensively investigated. Different views capture different information of point clouds and thus are complementary to each…

Traditional reinforcement learning often struggles to generate diverse, high-reward solutions, especially in domains like drug design and black-box function optimization. Markov Chain Monte Carlo (MCMC) methods provide an alternative method…

This work introduces GeoDirDock (GDD), a novel approach to molecular docking that enhances the accuracy and physical plausibility of ligand docking predictions. GDD guides the denoising process of a diffusion model along geodesic paths…

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…

In structure-based drug design, accurately estimating the binding affinity between a candidate ligand and its protein receptor is a central challenge. Recent advances in artificial intelligence, particularly deep learning, have demonstrated…

Structure-based drug design involves finding ligand molecules that exhibit structural and chemical complementarity to protein pockets. Deep generative methods have shown promise in proposing novel molecules from scratch (de-novo design),…

Design of de novo biological sequences with desired properties, like protein and DNA sequences, often involves an active loop with several rounds of molecule ideation and expensive wet-lab evaluations. These experiments can consist of…

Analyzing the structure of proteins is a key part of understanding their functions and thus their role in biology at the molecular level. In addition, design new proteins in a methodical way is a major engineering challenge. In this work,…

The performance of sensor arrays in sensing and wireless communications improves with more elements, but this comes at the cost of increased energy consumption and hardware expense. This work addresses the challenge of selecting $k$ sensor…

The challenge of discovering new molecules with desired properties is crucial in domains like drug discovery and material design. Recent advances in deep learning-based generative methods have shown promise but face the issue of sample…

Structure-Based Drug Design (SBDD) is a powerful strategy in computational drug discovery, utilizing three-dimensional protein structures to guide the design of molecules with improved binding affinity. However, capturing complex…

We present GFlowState, a visual analytics system designed to illuminate the training process of Generative Flow Networks (GFlowNets or GFNs). GFlowNets are a probabilistic framework for generating samples proportionally to a reward…

Generative Flow Networks (or GFlowNets for short) are a family of probabilistic agents that learn to sample complex combinatorial structures through the lens of "inference as control". They have shown great potential in generating…