Related papers: Towards Precision Protein-Ligand Affinity Predicti…

Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions. This paper introduces DeepProtein, a comprehensive and user-friendly deep…

The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…

DNA-binding proteins are a class of proteins which have a specific or general affinity to DNA and include three important components: transcription factors; nucleases, and histones. DNA-binding proteins also perform important roles in many…

Applying deep learning concepts from image detection and graph theory has greatly advanced protein-ligand binding affinity prediction, a challenge with enormous ramifications for both drug discovery and protein engineering. We build upon…

Predicting protein-ligand binding affinity is an essential part of computer-aided drug design. However, generalisable and performant global binding affinity models remain elusive, particularly in low data regimes. Despite the evolution of…

Accurately determining a change in protein binding affinity upon mutations is important for the discovery and design of novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations…

The structure of proteins is the basis for studying protein function and drug design. The emergence of AlphaFold 2 has greatly promoted the prediction of protein 3D structures, and it is of great significance to give an overall and accurate…

One key task in virtual screening is to accurately predict the binding affinity ($\triangle$$G$) of protein-ligand complexes. Recently, deep learning (DL) has significantly increased the predicting accuracy of scoring functions due to the…

Dynamic Algorithm Configuration (DAC) aims to dynamically control a target algorithm's hyperparameters in order to improve its performance. Several theoretical and empirical results have demonstrated the benefits of dynamically controlling…

Motivation: Protein-ligand affinity prediction is an important part of structure-based drug design. It includes molecular docking and affinity prediction. Although molecular dynamics can predict affinity with high accuracy at present, it is…

The development of modern Artificial Intelligence (AI) models, particularly diffusion-based models employed in computer vision and image generation tasks, is undergoing a paradigmatic shift in development methodologies. Traditionally…

The role of Artificial Intelligence (AI) is growing in every stage of drug development. Nevertheless, a major challenge in drug discovery AI remains: Drug pharmacokinetic (PK) and Drug-Target Interaction (DTI) datasets collected in…

We describe the accurate prediction of ligand-protein interaction (LPI) affinities, also known as drug-target interactions (DTI), with instruction fine-tuned pretrained generative small language models (SLMs). We achieved accurate…

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…

The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…

The field of drug discovery hinges on the accurate prediction of binding affinity between prospective drug molecules and target proteins, especially when such proteins directly influence disease progression. However, estimating binding…

The accurate prediction of protein-ligand binding affinity is important for drug discovery yet remains challenging for multi-domain proteins, where inter-domain dynamics and flexible linkers govern molecular recognition. Current geometric…

Protein solubility plays a critical role in improving production yield of recombinant proteins in biocatalyst and pharmaceutical field. To some extent, protein solubility can represent the function and activity of biocatalysts which are…

Multiple sequence alignment (MSA) data play a crucial role in the study of protein mutations, with contact prediction being a notable application. Existing methods are often model-based or algorithmic and typically do not incorporate…

Domain adaptation (DA) is a technique that transfers predictive models trained on a labeled source domain to an unlabeled target domain, with the core difficulty of resolving distributional shift between domains. Currently, most popular DA…