AIMC Topic: Protein Binding

Clear Filters Showing 1 to 10 of 954 articles

PANTHER Score: Protein-Affinity for Nucleic Target-binding, Hybridization, and Energy Regression.

RNA (New York, N.Y.) Jan 16, 2026
Although protein-RNA interactions are crucial for many biological processes, predicting their binding free energies (ΔG) is a challenging task due to limited available experimental data and the complexity of these interactions. To address this issue,...
RNA Machine Learning Nucleic Acid Hybridization Protein Binding Thermodynamics RNA-Binding Proteins Molecular Dynamics Simulation
View on PubMed DOI

Computational design of protein complexes: influence of binding affinity.

Chemical communications (Cambridge, England) Jan 13, 2026
The interaction of proteins with diverse molecular partners, including other proteins, nucleic acids, and carbohydrates, is essential for performing various functions, from signal transduction and gene regulation to immune recognition and cellular tr...
Protein Binding DNA Machine Learning Proteins Models, Molecular RNA Deep Learning
View on PubMed DOI

Leak Proof PDBBind: A Reorganized Data Set of Protein-Ligand Complexes for More Generalizable Binding Affinity Prediction.

The journal of physical chemistry. B Jan 4, 2026
The majority of machine learning scoring functions used in drug discovery for predicting protein-ligand binding poses and affinities have been trained on the PDBBind data set. However, it is unclear whether these new scoring functions are actually an...
Machine Learning Molecular Docking Simulation Protein Binding Ligands Binding Sites Proteins Thermodynamics Databases, Protein
View on PubMed DOI

Structure-Aware Heterogeneous Information Fusion Framework for Protein-Ligand Binding Affinity Prediction.

Journal of chemical information and modeling Dec 24, 2025
Accurate prediction of protein-ligand binding affinities (PLAs) is essential for drug discovery and development. Recent advancements suggest that transforming protein-ligand complexes into heterogeneous graph representations may offer a viable soluti...
Proteins Drug Discovery Ligands Protein Binding Neural Networks, Computer
View on PubMed DOI

Flexible protein-ligand docking with diffusion-based side-chain packing.

Proceedings of the National Academy of Sciences of the United States of America Dec 24, 2025
Understanding protein structure and dynamics is crucial for basic biology and drug design. Conventional methods often provide static conformations that inadequately capture protein flexibility. We present PackDock, a framework that integrates deep le...
Molecular Docking Simulation Deep Learning Protein Conformation Binding Sites Diffusion Protein Binding Ligands Proteins
View on PubMed DOI

Exploring Multi-Scale Interaction Features through a Physics-Aware Graph Network for Enhanced Binding Affinity Prediction.

Journal of chemical information and modeling Dec 23, 2025
Protein-ligand binding affinity plays a central role in molecular recognition and drug discovery, yet accurate prediction remains challenging due to the complexity of three-dimensional interactions. Conventional computational approaches, including do...
Neural Networks, Computer Ligands Protein Binding Proteins
View on PubMed DOI

A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein-Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases.

Journal of chemical information and modeling Dec 22, 2025
The accurate prediction of protein-ligand binding poses and affinities is central to structure-based drug design. In this study, we first benchmarked three distinct pose generation strategies for data sets from the ASAP Antiviral Challenge 2025: mole...
Coronavirus 3C Proteases Middle East Respiratory Syndrome Coronavirus Binding Sites Deep Learning Antiviral Agents Ligands Protein Conformation Protein Binding SARS-CoV-2 Molecular Docking Simulation Humans
View on PubMed DOI

Multiplex mapping of protein-protein interaction interfaces.

Proceedings of the National Academy of Sciences of the United States of America Dec 22, 2025
We describe peptide mapping through Split Antibiotic Resistance Complementation (SpARC-map), a method to identify the probable interface between two interacting proteins. Our method is based on in vivo affinity selection inside a bacterial host and u...
Proto-Oncogene Proteins c-mdm2 Humans High-Throughput Nucleotide Sequencing Protein Interaction Mapping Protein Binding
View on PubMed DOI

In silico-driven protocol for hit-to-lead optimization: a case study on PDE9A inhibitors.

Journal of computer-aided molecular design Dec 19, 2025
Hit-to-lead (H2L) optimization is a critical stage in small-molecule drug discovery, where efficient exploration of chemical space is required to identify promising lead compounds. Conventional H2L workflows rely on iterative synthesis and experiment...
Computer Simulation 3',5'-Cyclic-AMP Phosphodiesterases Molecular Docking Simulation Humans Drug Discovery Drug Design Small Molecule Libraries Machine Learning Structure-Activity Relationship Protein Binding Phosphodiesterase Inhibitors Thermodynamics
View on PubMed DOI

LGABAN: An Integrated Multi-Scale Approach Combining Graph and Sequence Features for Enhanced Prediction of Drug-Protein Interactions.

Journal of chemical information and modeling Dec 17, 2025
The accurate identification of drug-target interactions is crucial for shortening the timeline and lowering the expenses of pharmaceutical research, as the discovery of novel drugs remains a highly complex, resource-intensive, and lengthy endeavor. D...
Proteins Pharmaceutical Preparations Drug Discovery Deep Learning Humans Protein Binding
View on PubMed DOI
Popular Topics
Recent Journals