AIMC Topic: Allosteric Regulation

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'Intelligent' proteins.

Cellular and molecular life sciences : CMLS Jun 14, 2025
We present an idea of protein molecules that challenges the traditional view of proteins as simple molecular machines and suggests instead that they exhibit a basic form of "intelligence". The idea stems from suggestions coming from Integrated Inform...
Proteins Protein Conformation Allosteric Regulation Humans
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Molecular insights into the unique activation and allosteric modulation mechanisms of the human mas-related G-protein-coupled receptor X1.

International journal of biological macromolecules May 30, 2025
MRGPRX1 plays dual roles in mediating nociception and pruritus, making it a promising target for alleviating itch and inhibiting pain. However, the mechanisms underlying MRGPRX1 activation and allosteric modulation remain poorly understood, posing si...
Molecular Dynamics Simulation Protein Conformation Binding Sites Receptors, Neuropeptide Receptors, G-Protein-Coupled Allosteric Regulation Humans Protein Binding
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Therapeutic potential of allosteric HECT E3 ligase inhibition.

Cell Apr 2, 2025
Targeting ubiquitin E3 ligases is therapeutically attractive; however, the absence of an active-site pocket impedes computational approaches for identifying inhibitors. In a large, unbiased biochemical screen, we discover inhibitors that bind a crypt...
Humans Animals Allosteric Regulation Signal Transduction Pulmonary Arterial Hypertension Male Ubiquitin-Protein Ligases Ubiquitination Mice Bone Morphogenetic Protein Receptors, Type II
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Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?

Journal of chemical information and modeling Apr 1, 2025
Allosteric compounds offer an alternative mode of inhibition to orthosteric compounds with opportunities for selectivity and noncompetition. Structure-based drug design (SBDD) of allosteric compounds introduces complications compared to their orthost...
Deep Learning Ligands Protein Conformation Molecular Docking Simulation Drug Design Allosteric Regulation Protein Kinase Inhibitors Cyclin-Dependent Kinase 2
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Identification of Novel Fourth-Generation Allosteric Inhibitors Targeting Inactive State of EGFR T790M/L858R/C797S and T790M/L858R Mutations: A Combined Machine Learning and Molecular Dynamics Approach.

The journal of physical chemistry. B Mar 7, 2025
Targeted therapy with an allosteric inhibitor (AIs) is an important area of research in patients with epidermal growth factor receptor (EGFR) mutations. Current treatment of nonsmall cell lung cancer patients with EGFR mutations using orthosteric inh...
Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Protein Kinase Inhibitors Allosteric Regulation ErbB Receptors Machine Learning Mutation Humans
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Study on SHP2 Conformational Transition and Structural Characterization of Its High-Potency Allosteric Inhibitors by Molecular Dynamics Simulations Combined with Machine Learning.

Molecules (Basel, Switzerland) Dec 24, 2024
The src-homology 2 domain-containing phosphatase 2 (SHP2) is a human cytoplasmic protein tyrosine phosphatase that plays a crucial role in cellular signal transduction. Aberrant activation and mutations of SHP2 are associated with tumor growth and im...
Machine Learning Protein Binding Enzyme Inhibitors Protein Conformation Molecular Dynamics Simulation Humans Allosteric Regulation Protein Tyrosine Phosphatase, Non-Receptor Type 11
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MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data.

Genome biology Dec 2, 2024
We present MoCHI, a tool to fit interpretable models using deep mutational scanning data. MoCHI infers free energy changes, as well as interaction terms (energetic couplings) for specified biophysical models, including from multimodal phenotypic data...
Allosteric Regulation Software Models, Genetic Thermodynamics Epistasis, Genetic Humans Mutation Neural Networks, Computer Machine Learning
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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 Allosteric Regulation Machine Learning Protein Conformation Receptors, Adrenergic, beta-2 Drug Design Humans Molecular Dynamics Simulation
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Adaptive Workflows of Machine Learning Illuminate the Sequential Operation Mechanism of the TAK1's Allosteric Network.

Biochemistry May 14, 2024
Allostery is a fundamental mechanism driving biomolecular processes that holds significant therapeutic concern. Our study rigorously investigates how two distinct machine-learning algorithms uniquely classify two already close-to-active DFG-in states...
Molecular Dynamics Simulation Humans Protein Conformation Machine Learning Allosteric Regulation Algorithms MAP Kinase Kinase Kinases Workflow
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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...
Binding Sites Allosteric Site Allosteric Regulation Proteins Artificial Intelligence Ligands Machine Learning
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