AIMC Topic: Ligands

Clear Filters Showing 521 to 530 of 660 articles

First report on analysis of chemical space, scaffold diversity, critical structural features of HDAC11 inhibitors.

Molecular diversity Aug 1, 2025
In the histone deacetylase (HDAC) family, HDAC11 is the smallest and a single member under the class IV subtype. It is important as a drug target mainly in cancer, inflammatory and autoimmune diseases. The design and development of selective HDAC11 i...
Quantitative Structure-Activity Relationship Histone Deacetylase Inhibitors Histone Deacetylases Molecular Structure Molecular Dynamics Simulation Ligands Molecular Docking Simulation Drug Design Humans
View on PubMed DOI

TopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability Prediction.

Journal of molecular biology Aug 1, 2025
Development of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines being attractive targets due to their nucleophilicity and relative scarcity. While structural biology ...
Ligands Humans Cysteine Machine Learning Proteomics Proteome Databases, Protein
View on PubMed DOI

Multi-omics identifies OSM-OSMR as a key receptor-ligand in the tumor environment of endometrial adenocarcinoma.

International immunopharmacology Jul 28, 2025
Endometrial adenocarcinoma carries a bleak prognosis, and the molecular markers that evaluate the progression of endometrial adenocarcinoma to advanced stages remain uncertain. Cell-cell communication plays a crucial role in the tumor microenvironmen...
Ligands Endometrial Neoplasms Oncostatin M Signal Transduction Adenocarcinoma Mice, Nude Oncostatin M Receptor beta Subunit Transcriptome Cell Line, Tumor Mice Multiomics Gene Expression Regulation, Neoplastic Cell Proliferation Tumor Microenvironment Animals Gene Expression Profiling Humans Prognosis Female
View on PubMed DOI

Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands.

Angewandte Chemie (International ed. in English) Jul 28, 2025
The challenge of targeting RNA with small molecules necessitates a better understanding of RNA-ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand-induced stabilization, and how conformational changes influence g...
Aminoimidazole Carboxamide Nucleic Acid Conformation Machine Learning Ribonucleotides Molecular Dynamics Simulation Riboswitch Ligands
View on PubMed DOI

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.

Journal of chemical information and modeling Jul 14, 2025
A critical assessment of computational hit-finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comprised of co...
Humans RNA Helicases Protein Binding RNA, Viral Ligands Viral Nonstructural Proteins Binding Sites Molecular Docking Simulation Machine Learning COVID-19 Drug Treatment Drug Discovery COVID-19 Methyltransferases Antiviral Agents SARS-CoV-2
View on PubMed DOI

CAML: Commutative Algebra Machine Learning─A Case Study on Protein-Ligand Binding Affinity Prediction.

Journal of chemical information and modeling Jul 14, 2025
Recently, Suwayyid and Wei introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we propose commutative algebra machine learning (CAML) for the prediction of protein-ligand binding affinities. Spe...
Protein Binding Proteins Ligands Machine Learning Algorithms
View on PubMed DOI

Computer-Aided Drug Discovery for Undruggable Targets.

Chemical reviews Jul 9, 2025
Undruggable targets are those of therapeutical significance but challenging for conventional drug design approaches. Such targets often exhibit unique features, including highly dynamic structures, a lack of well-defined ligand-binding pockets, the p...
Computer-Aided Design Drug Design Drug Discovery Intrinsically Disordered Proteins Allosteric Regulation Humans Proteins Artificial Intelligence Ligands
View on PubMed DOI

AIoptamer: Artificial Intelligence-Driven Aptamer Optimization Pipeline for Targeted Therapeutics in Healthcare.

Molecular pharmaceutics Jul 7, 2025
Aptamers are short, single-stranded DNA or RNA molecules known for their high specificity and affinity toward target biomolecules, making them powerful tools in drug discovery, diagnostics, and biosensing. However, conventional aptamer selection meth...
Artificial Intelligence Machine Learning Drug Discovery Humans SELEX Aptamer Technique Deep Learning Aptamers, Nucleotide Ligands
View on PubMed DOI

PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.

Nucleic acids research Jul 7, 2025
Knowledge of protein-ligand binding sites (LBSs) is crucial for advancing our understanding of biology and developing practical applications in fields such as medicine or biotechnology. PrankWeb is a web server that allows users to predict LBSs from ...
Machine Learning Software Molecular Docking Simulation User-Computer Interface Protein Binding Binding Sites Proteins Internet Ligands Protein Conformation
View on PubMed DOI

InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep.

Nucleic acids research Jul 7, 2025
Predicting functional binding sites in proteins is crucial for understanding protein-protein interactions (PPIs) and identifying drug targets. While various computational approaches exist, many fail to assess PPI ligandability, which often involves c...
Protein Binding Computational Biology Proteins Software Deep Learning Ligands Protein Conformation Binding Sites Protein Interaction Mapping Databases, Protein Models, Molecular Internet
View on PubMed DOI
Popular Topics
Recent Journals