AIMC Topic: Allosteric Regulation

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Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1.

The journal of physical chemistry. B Dec 28, 2020
Allosteric molecules provide a powerful means to modulate protein function. However, the effect of such ligands on distal orthosteric sites cannot be easily described by classical docking methods. Here, we applied machine learning (ML) approaches to ...
Allosteric Site Allosteric Regulation Ligands Molecular Chaperones Machine Learning Molecular Dynamics Simulation
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Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites.

Proteins Jun 22, 2019
Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity or regulatory binding sites (allosteric sites), that modulate the activity of functional binding sites throu...
Binding Sites Allosteric Site Allosteric Regulation Molecular Dynamics Simulation Protein Conformation Proteins Databases, Protein Protein Binding Humans Algorithms Artificial Intelligence Evolution, Molecular Machine Learning
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Prediction of Orthosteric and Allosteric Regulations on Cannabinoid Receptors Using Supervised Machine Learning Classifiers.

Molecular pharmaceutics May 3, 2019
Designing highly selective compounds to protein subtypes and developing allosteric modulators targeting them are critical considerations to both drug discovery and mechanism studies for cannabinoid receptors. It is challenging but in demand to have c...
Machine Learning Algorithms Humans Allosteric Regulation Receptors, Cannabinoid Animals Support Vector Machine
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Perturbation Theory/Machine Learning Model of ChEMBL Data for Dopamine Targets: Docking, Synthesis, and Assay of New l-Prolyl-l-leucyl-glycinamide Peptidomimetics.

ACS chemical neuroscience Jun 25, 2018
Predicting drug-protein interactions (DPIs) for target proteins involved in dopamine pathways is a very important goal in medicinal chemistry. We can tackle this problem using Molecular Docking or Machine Learning (ML) models for one specific protein...
Neural Networks, Computer Allosteric Regulation MSH Release-Inhibiting Hormone Machine Learning Peptidomimetics Deep Learning Humans Databases, Chemical Receptors, Dopamine D2 Models, Molecular Dopamine Software Nonlinear Dynamics Molecular Docking Simulation
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Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning.

Journal of biomolecular structure & dynamics Mar 2, 2018
Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associ...
Allosteric Regulation Molecular Dynamics Simulation Sodium Protein Binding Hydrogen Bonding Protein Conformation Humans Mutation Thrombin Machine Learning
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Deep learning-guided design of dynamic proteins.

Science (New York, N.Y.) May 22, 2025
Deep learning has advanced the design of static protein structures, but the controlled conformational changes that are hallmarks of natural signaling proteins have remained inaccessible to de novo design. Here, we describe a general deep learning-gui...
Deep Learning Proteins Mutation Protein Conformation Protein Engineering Allosteric Regulation Molecular Dynamics Simulation Ligands
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ASD2023: towards the integrating landscapes of allosteric knowledgebase.

Nucleic acids research Jan 5, 2024
Allosteric regulation, induced by perturbations at an allosteric site topographically distinct from the orthosteric site, is one of the most direct and efficient ways to fine-tune macromolecular function. The Allosteric Database (ASD; accessible onli...
Allosteric Site Allosteric Regulation Drug Discovery Protein Interaction Maps Humans Proteome Knowledge Bases Ligands
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DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations.

Nucleic acids research Jul 5, 2023
Driver mutations can contribute to the initial processes of cancer, and their identification is crucial for understanding tumorigenesis as well as for molecular drug discovery and development. Allostery regulates protein function away from the functi...
Animals Mice Proteins Carcinogenesis Neoplasms Deep Learning Allosteric Regulation Mutation Allosteric Site
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