AIMC Topic: Ligands

Clear Filters Showing 51 to 60 of 659 articles

Natural Language Processing Methods for the Study of Protein-Ligand Interactions.

Journal of chemical information and modeling Feb 24, 2025
Natural Language Processing (NLP) has revolutionized the way computers are used to study and interact with human languages and is increasingly influential in the study of protein and ligand binding, which is critical for drug discovery and developmen...
Natural Language Processing Ligands Drug Discovery Protein Binding Proteins Humans Machine Learning
View on PubMed DOI

T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment.

Journal of chemical information and modeling Feb 18, 2025
There is significant interest in targeting disease-causing proteins with small molecule inhibitors to restore healthy cellular states. The ability to accurately predict the binding affinity of small molecules to a protein target in silico enables the...
Protein Binding Proteins Ligands Drug Discovery Deep Learning ErbB Receptors Uncertainty Neural Networks, Computer SARS-CoV-2 Humans
View on PubMed DOI

CL-GNN: Contrastive Learning and Graph Neural Network for Protein-Ligand Binding Affinity Prediction.

Journal of chemical information and modeling Feb 6, 2025
In the realm of drug discovery and design, the accurate prediction of protein-ligand binding affinity is of paramount importance as it underpins the functional interactions within biological systems. This study introduces a novel self-supervised lear...
Neural Networks, Computer Ligands Machine Learning Graph Neural Networks Protein Binding Drug Discovery Proteins
View on PubMed DOI

Protein ligand structure prediction: From empirical to deep learning approaches.

Current opinion in structural biology Feb 5, 2025
Protein-ligand structure prediction methods, aiming to predict the three-dimensional complex structure and binding energy of a compound and target protein, are essential in many structure-based drug discovery pipelines, including virtual screening an...
Drug Discovery Deep Learning Protein Binding Models, Molecular Computational Biology Ligands Protein Conformation Proteins
View on PubMed DOI

PPARγ modulator predictor (PGMP_v1): chemical space exploration and computational insights for enhanced type 2 diabetes mellitus management.

Molecular diversity Feb 1, 2025
Peroxisome proliferator-activated receptor gamma (PPARγ) plays a critical role in adipocyte differentiation and enhances insulin sensitivity. In contemporary drug discovery, in silico design strategies offer significant advantages by revealing essent...
Humans Molecular Docking Simulation Drug Design Hypoglycemic Agents Ligands PPAR gamma Drug Discovery Diabetes Mellitus, Type 2
View on PubMed DOI

The prediction of RNA-small-molecule ligand binding affinity based on geometric deep learning.

Computational biology and chemistry Jan 29, 2025
Small molecule-targeted RNA is an emerging technology that plays a pivotal role in drug discovery and inhibitor design, with widespread applications in disease treatment. Consequently, predicting RNA-small-molecule ligand interactions is crucial. Wit...
Small Molecule Libraries Ligands Binding Sites Deep Learning RNA
View on PubMed DOI

Transformer Decoder Learns from a Pretrained Protein Language Model to Generate Ligands with High Affinity.

Journal of chemical information and modeling Jan 27, 2025
The drug discovery process can be significantly accelerated by using deep learning methods to suggest molecules with druglike features and, more importantly, that are good candidates to bind specific proteins of interest. We present a novel deep lear...
Models, Molecular Ligands Drug Discovery Deep Learning Protein Binding Proteins
View on PubMed DOI

DisDock: A Deep Learning Method for Metal Ion-Protein Redocking.

Proteins Jan 22, 2025
The structures of metalloproteins are essential for comprehending their functions and interactions. The breakthrough of AlphaFold has made it possible to predict protein structures with experimental accuracy. However, the type of metal ion that a met...
Protein Conformation Binding Sites Metalloproteins Ions Ligands Software Algorithms Molecular Docking Simulation Protein Binding Deep Learning Computational Biology Metals Databases, Protein
View on PubMed DOI

Active Learning to Select the Most Suitable Reagents and One-Step Organic Chemistry Reactions for Prioritizing Target-Specific Hits from Ultralarge Chemical Spaces.

Journal of chemical information and modeling Jan 16, 2025
Designing chemically novel and synthesizable ligands from the largest possible chemical space is a major issue in modern drug discovery to identify early hits that are easily amenable to medicinal chemistry optimization. Starting from the sole three-...
Machine Learning Molecular Docking Simulation Proteins Ligands Drug Discovery Indicators and Reagents
View on PubMed DOI

Targeting protein-ligand neosurfaces with a generalizable deep learning tool.

Nature Jan 15, 2025
Molecular recognition events between proteins drive biological processes in living systems. However, higher levels of mechanistic regulation have emerged, in which protein-protein interactions are conditioned to small molecules. Despite recent advanc...
Proteins Drug Design Proto-Oncogene Proteins c-bcl-2 Models, Molecular Humans Ligands Bridged Bicyclo Compounds, Heterocyclic Deep Learning Protein Binding
View on PubMed DOI
Popular Topics
Recent Journals