Related papers: Decoding the Protein-ligand Interactions Using Par…

Introduction Accurate prediction of protein-protein interactions (PPIs) is crucial for understanding cellular functions and advancing drug development. Existing in-silico methods use direct sequence embeddings from Protein Language Models…

Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in…

Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere…

Is it feasible to create an analysis paradigm that can analyze and then accurately and quickly predict known drugs from experimental data? PharML.Bind is a machine learning toolkit which is able to accomplish this feat. Utilizing deep…

Accurately predicting drug-target interactions (DTIs) is pivotal for advancing drug discovery and target validation techniques. While machine learning approaches including those that are based on Graph Neural Networks (GNN) have achieved…

Since multidrug combination is widely applied, the accurate prediction of drug-drug interaction (DDI) is becoming more and more critical. In our method, we use graph to represent drug-drug interaction: nodes represent drug; edges represent…

Molecular interaction networks are powerful resources for the discovery. They are increasingly used with machine learning methods to predict biologically meaningful interactions. While deep learning on graphs has dramatically advanced the…

Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…

Modeling the effects of mutations on the binding affinity plays a crucial role in protein engineering and drug design. In this study, we develop a novel deep learning based framework, named GraphPPI, to predict the binding affinity changes…

Identifying protein functional sites (PFSs) and protein-ligand interactions (PLIs) are critically important in understanding the protein function and the involved biochemical reactions. As large amount of unknown proteins are quickly…

Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which amino-acid residues are in close spatial proximity given the amino-acid sequence…

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability…

Motivation: Exploring drug-protein interactions (DPIs) work as a pivotal step in drug discovery. The fast expansion of available biological data enables computational methods effectively assist in experimental methods. Among them, deep…

Accurate prediction of drug-drug interactions (DDI) is crucial for medication safety and effective drug development. However, existing methods often struggle to capture structural information across different scales, from local functional…

Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently,…

Protein function prediction may be framed as predicting subgraphs (with certain closure properties) of a directed acyclic graph describing the hierarchy of protein functions. Graph neural networks (GNNs), with their built-in inductive bias…

The prediction of protein interactions (CPIs) is crucial for the in-silico screening step in drug discovery. Recently, many end-to-end representation learning methods using deep neural networks have achieved significantly better performance…

Being able to identify regions within or around proteins, to which ligands can potentially bind, is an essential step to develop new drugs. Binding site identification methods can now profit from the availability of large amounts of 3D…

Graph neural networks (GNNs) constitute a class of deep learning methods for graph data. They have wide applications in chemistry and biology, such as molecular property prediction, reaction prediction and drug-target interaction…

Prediction of protein-ligand (PL) binding affinity remains the key to drug discovery. Popular approaches in recent years involve graph neural networks (GNNs), which are used to learn the topology and geometry of PL complexes. However, GNNs…