AIMC Topic: Protein Binding

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A Bayesian Optimization-Based Hybrid Deep Prediction Method for Zinc-Binding Protein Interaction Sites.

Journal of chemical information and modeling Jul 14, 2025
The binding of zinc ions to proteins plays a crucial role in normal physiological functions and life activities of organisms. To enhance the prediction accuracy of zinc-binding protein interaction sites, the paper proposes a novel hybrid deep predict...
Carrier Proteins Bayes Theorem Binding Sites Zinc Protein Binding Computational Biology
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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...
Viral Nonstructural Proteins Binding Sites RNA Helicases Ligands COVID-19 Drug Treatment Methyltransferases SARS-CoV-2 Molecular Docking Simulation Drug Discovery Antiviral Agents Protein Binding RNA, Viral Humans Machine Learning COVID-19
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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...
Proteins Ligands Machine Learning Algorithms Protein Binding
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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 Ligands Software Protein Binding Protein Conformation Molecular Docking Simulation Binding Sites Proteins User-Computer Interface Internet
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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...
Databases, Protein Models, Molecular Protein Interaction Mapping Internet Software Protein Binding Deep Learning Computational Biology Ligands Proteins Protein Conformation Binding Sites
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HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.

Nucleic acids research Jul 7, 2025
Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integ...
Deep Learning Protein Binding Computational Biology Software Molecular Docking Simulation Protein Conformation Protein Interaction Mapping Multiprotein Complexes Proteins Mutation Internet
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Prediction of Specificity of α-Conotoxins to Subtypes of Human Nicotinic Acetylcholine Receptors with Semi-supervised Machine Learning.

ACS chemical neuroscience Jun 18, 2025
Conotoxins are a family of highly toxic neurotoxins composed of cysteine-rich peptides produced by marine cone snails. The most lethal cone snail species to humans is with fatality rates of up to ∼65% from a single sting, which is caused mostly by t...
Supervised Machine Learning Amino Acid Sequence Conotoxins Receptors, Nicotinic Conus Snail Humans Machine Learning Protein Binding
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DTBA-net: Drug-Target Binding Affinity prediction using feature selection in hybrid CNN model.

Journal of computer-aided molecular design Jun 16, 2025
In drug discovery, virtual screening and repositioning rely on accurate Drug-Target Binding Affinity (DTBA) prediction to develop effective therapies. However, DTBA prediction remains challenging due to limited annotated datasets, high-dimensional bi...
Drug Discovery Proteins Deep Learning Protein Binding Binding Sites Humans Neural Networks, Computer Algorithms
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Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities.

Journal of chemical information and modeling Jun 9, 2025
The leucine-rich repeat kinase 2 (LRRK2) is the most mutated gene in familial Parkinson's disease, and its mutations lead to pathogenic hallmarks of the disease. The LRRK2 WDR domain is an understudied drug target for Parkinson's disease, with no kno...
Protein Binding Ligands Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 Humans Protein Domains Machine Learning Protein Kinase Inhibitors Molecular Dynamics Simulation Thermodynamics
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Investigating the Nature of PRM:SH3 Interactions Using Artificial Intelligence and Molecular Dynamics.

Journal of chemical information and modeling Jun 9, 2025
Understanding the binding interactions within protein-peptide complexes is crucial for elucidating key physicochemical phenomena in biological systems. Among the outcomes of these interactions, biomolecular condensates have recently emerged as vital ...
Molecular Dynamics Simulation Artificial Intelligence Hydrophobic and Hydrophilic Interactions Peptides src Homology Domains Protein Binding Mutation
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