AIMC Topic: Allosteric Site

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Challenge for Deep Learning: Protein Structure Prediction of Ligand-Induced Conformational Changes at Allosteric and Orthosteric Sites.

Journal of chemical information and modeling Nov 1, 2024
In the realm of biomedical research, understanding the intricate structure of proteins is crucial, as these structures determine how proteins function within our bodies and interact with potential drugs. Traditionally, methods like X-ray crystallogra...
Deep Learning Ligands Protein Conformation Allosteric Site Databases, Protein Models, Molecular Proteins
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Integrative residue-intuitive machine learning and MD Approach to Unveil Allosteric Site and Mechanism for β2AR.

Nature communications Sep 16, 2024
Allosteric drugs offer a new avenue for modern drug design. However, the identification of cryptic allosteric sites presents a formidable challenge. Following the allostery nature of residue-driven conformation transition, we propose a state-of-the-a...
Allosteric Site Humans Allosteric Regulation Drug Design Machine Learning Molecular Dynamics Simulation Protein Conformation Receptors, Adrenergic, beta-2
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Machine learning approaches in predicting allosteric sites.

Current opinion in structural biology Feb 13, 2024
Allosteric regulation is a fundamental biological mechanism that can control critical cellular processes via allosteric modulator binding to protein distal functional sites. The advantages of allosteric modulators over orthosteric ones have sparked t...
Artificial Intelligence Allosteric Regulation Ligands Machine Learning Binding Sites Allosteric Site Proteins
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From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on "Allosteric Intersection" of Biochemical and Big Data Approaches.

International journal of molecular sciences Apr 24, 2023
The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approach...
Allosteric Site Big Data Proteins Artificial Intelligence Deep Learning
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Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model.

Journal of chemical information and modeling Apr 14, 2023
Allosteric modulators are important regulation elements that bind the allosteric site beyond the active site, leading to the changes in dynamic and/or thermodynamic properties of the protein. Allosteric modulators have been a considerable interest as...
Deep Learning Proteins Allosteric Site Allosteric Regulation Molecular Dynamics Simulation Catalytic Domain
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AlphaFold, allosteric, and orthosteric drug discovery: Ways forward.

Drug discovery today Mar 11, 2023
Drug discovery is arguably a highly challenging and significant interdisciplinary aim. The stunning success of the artificial intelligence-powered AlphaFold, whose latest version is buttressed by an innovative machine-learning approach that integrate...
Proteins Allosteric Site Allosteric Regulation Artificial Intelligence Drug Design Drug Discovery
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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 Machine Learning Ligands Molecular Chaperones Molecular Dynamics Simulation
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers.

Progress in molecular biology and translational science Dec 6, 2019
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfam...
Computational Biology Support Vector Machine Mutation Molecular Dynamics Simulation Receptors, G-Protein-Coupled Allosteric Site Crystallography, X-Ray Algorithms Humans Protein Multimerization Protein Interaction Mapping Animals Neural Networks, Computer Machine Learning Protein Structure, Secondary Protein Binding Software Ligands Fluorescence Resonance Energy Transfer
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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...
Databases, Protein Humans Algorithms Machine Learning Molecular Dynamics Simulation Protein Binding Allosteric Regulation Evolution, Molecular Artificial Intelligence Binding Sites Protein Conformation Proteins Allosteric Site
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Recognition of protein allosteric states and residues: Machine learning approaches.

Journal of computational chemistry Mar 31, 2018
Allostery is a process by which proteins transmit the effect of perturbation at one site to a distal functional site upon certain perturbation. As an intrinsically global effect of protein dynamics, it is difficult to associate protein allostery with...
Proteins Neural Networks, Computer Molecular Dynamics Simulation Machine Learning Allosteric Site
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