Related papers: What Ails Generative Structure-based Drug Design: …

Graph generation poses a significant challenge as it involves predicting a complete graph with multiple nodes and edges based on simply a given label. This task also carries fundamental importance to numerous real-world applications,…

Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets. Generative SBDD methods leverage structural data of drugs in complex with their protein…

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although current graph…

Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…

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…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Graph Neural Networks (GNNs) are powerful tools for learning on structured data, yet the relationship between their expressivity and predictive performance remains unclear. We introduce a family of premetrics that capture different degrees…

Generative models for structure-based molecular design hold significant promise for drug discovery, with the potential to speed up the hit-to-lead development cycle, while improving the quality of drug candidates and reducing costs. Data…

Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph…

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…

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,…

While Graph Neural Networks (GNNs) have achieved remarkable results in a variety of applications, recent studies exposed important shortcomings in their ability to capture the structure of the underlying graph. It has been shown that the…

Graph neural networks (GNNs) have emerged as one of the most effective ML techniques for drug effect prediction from drug molecular graphs. Despite having immense potential, GNN models lack performance when using datasets that contain…

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…

Graph neural networks (GNNs) are effective machine learning models for many graph-related applications. Despite their empirical success, many research efforts focus on the theoretical limitations of GNNs, i.e., the GNNs expressive power.…

Expressivity and generalization are two critical aspects of graph neural networks (GNNs). While significant progress has been made in studying the expressivity of GNNs, much less is known about their generalization capabilities,…

The study of Graph Neural Networks has received considerable interest in the past few years. By extending deep learning to graph-structured data, GNNs can solve a diverse set of tasks in fields including social science, chemistry, and…

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…