AIMC Topic: Protein Binding

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Predicting protein-protein interaction with interpretable bilinear attention network.

Computer methods and programs in biomedicine Mar 30, 2025
BACKGROUND AND OBJECTIVE: Protein-protein interactions (PPIs) play the key roles in myriad biological processes, helping to understand the protein function and disease pathology. Identification of PPIs and their interaction types through wet experime...
Neural Networks, Computer Algorithms Deep Learning Humans Databases, Protein Amino Acid Sequence Protein Conformation Protein Binding Computational Biology Proteins Protein Interaction Mapping Sequence Analysis, Protein
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Molecular docking-QSAR-Kronecker-regularized least squares-based multiple machine learning for assessment and prediction of PFAS-protein binding interactions.

Journal of hazardous materials Mar 29, 2025
Ubiquitous per- and poly-fluoroalkyl substances (PFAS) threaten human's health and attract worldwide attention. PFAS-mediated toxicity involves adverse effects of PFAS on proteins, and assessment of PFAS-protein binding interactions helps to explain ...
PPAR gamma Humans Protein Binding Quantitative Structure-Activity Relationship Machine Learning Least-Squares Analysis Serum Albumin, Human Molecular Docking Simulation Fluorocarbons Prealbumin
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Atomic context-conditioned protein sequence design using LigandMPNN.

Nature methods Mar 28, 2025
Protein sequence design in the context of small molecules, nucleotides and metals is critical to enzyme and small-molecule binder and sensor design, but current state-of-the-art deep-learning-based sequence design methods are unable to model nonprote...
Protein Conformation Deep Learning Amino Acid Sequence Protein Binding Ligands Crystallography, X-Ray Proteins Models, Molecular
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Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning.

Physical chemistry chemical physics : PCCP Mar 26, 2025
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the ...
Cyclin-Dependent Kinase 6 Protein Binding Phosphorylation Molecular Dynamics Simulation Protein Conformation Protein Kinase Inhibitors Thermodynamics Humans Deep Learning
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Leveraging Transfer Learning for Predicting Protein-Small-Molecule Interaction Predictions.

Journal of chemical information and modeling Mar 24, 2025
A complex web of intermolecular interactions defines and regulates biological processes. Understanding this web has been particularly challenging because of the sheer number of actors in biological systems: ∼10 proteins in a typical human cell offer ...
Proteins Ligands Small Molecule Libraries Neural Networks, Computer Humans Machine Learning Protein Binding
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Mechanistic Study of Protein Interaction with Natto Inhibitory Peptides Targeting Xanthine Oxidase: Insights from Machine Learning and Molecular Dynamics Simulations.

Journal of chemical information and modeling Mar 24, 2025
Bioactive peptides from food sources offer a safe and biocompatible approach to enzyme inhibition, with potential applications in managing metabolic disorders such as hyperuricemia and gout, conditions linked to excessive xanthine oxidase activity. U...
Molecular Dynamics Simulation Humans Protein Binding Enzyme Inhibitors Machine Learning Bacillus subtilis Xanthine Oxidase Peptides
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Deep-ProBind: binding protein prediction with transformer-based deep learning model.

BMC bioinformatics Mar 22, 2025
Binding proteins play a crucial role in biological systems by selectively interacting with specific molecules, such as DNA, RNA, or peptides, to regulate various cellular processes. Their ability to recognize and bind target molecules with high speci...
Sequence Analysis, Protein Neural Networks, Computer Databases, Protein Algorithms Deep Learning Binding Sites Protein Binding Computational Biology Proteins
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PCANN Program for Structure-Based Prediction of Protein-Protein Binding Affinity: Comparison With Other Neural-Network Predictors.

Proteins Mar 21, 2025
In this communication, we introduce a new structure-based affinity predictor for protein-protein complexes. This predictor, dubbed PCANN (Protein Complex Affinity by Neural Network), uses the ESM-2 language model to encode the information about prote...
Software Algorithms Deep Learning Humans Neural Networks, Computer Databases, Protein Protein Binding Protein Conformation Computational Biology Binding Sites Proteins
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Binding mechanism of inhibitors to DFG-in and DFG-out P38α deciphered using multiple independent Gaussian accelerated molecular dynamics simulations and deep learning.

SAR and QSAR in environmental research Mar 20, 2025
P38α has been identified as a key target for drug design to treat a wide range of diseases. In this study, multiple independent Gaussian accelerated molecular dynamics (GaMD) simulations, deep learning (DL), and the molecular mechanics generalized Bo...
Quantitative Structure-Activity Relationship Mitogen-Activated Protein Kinase 14 Protein Binding Drug Design Molecular Dynamics Simulation Deep Learning
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Developing predictive models for µ opioid receptor binding using machine learning and deep learning techniques.

Experimental biology and medicine (Maywood, N.J.) Mar 19, 2025
Opioids exert their analgesic effect by binding to the µ opioid receptor (MOR), which initiates a downstream signaling pathway, eventually inhibiting pain transmission in the spinal cord. However, current opioids are addictive, often leading to overd...
Receptors, Opioid, mu Humans Machine Learning Deep Learning Protein Binding Support Vector Machine Structure-Activity Relationship Analgesics, Opioid Ligands
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