AIMC Topic: Protein Conformation

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A Mode Evolution Metric to Extract Reaction Coordinates for Biomolecular Conformational Transitions.

Journal of chemical theory and computation Sep 17, 2024
The complex, multidimensional energy landscape of biomolecules makes the extraction of suitable, nonintuitive collective variables (CVs) that describe their conformational transitions challenging. At present, dimensionality reduction approaches and m...
Thermodynamics Protein Conformation Monte Carlo Method Machine Learning Molecular Dynamics Simulation Dipeptides
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Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots.

Journal of chemical information and modeling Sep 16, 2024
Identifying druggable binding sites on proteins is an important and challenging problem, particularly for cryptic, allosteric binding sites that may not be obvious from X-ray, cryo-EM, or predicted structures. The Site-Identification by Ligand Compet...
Binding Sites Protein Binding Machine Learning Ligands Proteins Molecular Dynamics Simulation Protein Conformation Drug Discovery
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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...
Machine Learning Drug Design Protein Conformation Receptors, Adrenergic, beta-2 Molecular Dynamics Simulation Allosteric Site Humans Allosteric Regulation
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Modelling protein complexes with crosslinking mass spectrometry and deep learning.

Nature communications Sep 9, 2024
Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrate experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multim...
Mass Spectrometry Models, Molecular Deep Learning Bacillus subtilis Protein Conformation Cross-Linking Reagents Iron Bacterial Proteins
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Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.

International journal of molecular sciences Sep 8, 2024
Protein dynamics play a crucial role in biological function, encompassing motions ranging from atomic vibrations to large-scale conformational changes. Recent advancements in experimental techniques, computational methods, and artificial intelligence...
Molecular Dynamics Simulation Protein Conformation Magnetic Resonance Spectroscopy Cryoelectron Microscopy Nuclear Magnetic Resonance, Biomolecular Machine Learning Proteins Humans
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Teaching old docks new tricks with machine learning enhanced ensemble docking.

Scientific reports Sep 5, 2024
We here introduce Ensemble Optimizer (EnOpt), a machine-learning tool to improve the accuracy and interpretability of ensemble virtual screening (VS). Ensemble VS is an established method for predicting protein/small-molecule (ligand) binding. Unlike...
Machine Learning Ligands Protein Conformation Protein Binding Proteins Software Molecular Docking Simulation
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PCP-GC-LM: single-sequence-based protein contact prediction using dual graph convolutional neural network and convolutional neural network.

BMC bioinformatics Sep 2, 2024
BACKGROUND: Recently, the process of evolution information and the deep learning network has promoted the improvement of protein contact prediction methods. Nevertheless, still remain some bottleneck: (1) One of the bottlenecks is the prediction of o...
Databases, Protein Protein Conformation Computational Biology Proteins Sequence Analysis, Protein Algorithms Neural Networks, Computer Deep Learning
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A Deep Learning Approach to Uncover Voltage-Gated Ion Channels' Intermediate States.

The journal of physical chemistry. B Aug 30, 2024
Owing to recent advancements in cryo-electron microscopy, voltage-gated ion channels have gained a greater comprehension of their structural characteristics. However, a significant enigma remains unsolved for a large majority of these channels: their...
Kv1.2 Potassium Channel Protein Conformation Deep Learning Ion Channel Gating Molecular Dynamics Simulation
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The path to the G protein-coupled receptor structural landscape: Major milestones and future directions.

British journal of pharmacology Aug 29, 2024
G protein-coupled receptors (GPCRs) play a crucial role in cell function by transducing signals from the extracellular environment to the inside of the cell. They mediate the effects of various stimuli, including hormones, neurotransmitters, ions, ph...
Animals Receptors, G-Protein-Coupled Protein Conformation Humans
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Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning.

Journal of chemical information and modeling Aug 28, 2024
Binding of partners and mutations highly affects the conformational dynamics of KRAS4B, which is of significance for deeply understanding its function. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) and prin...
Molecular Dynamics Simulation Protein Conformation Principal Component Analysis Mutation Humans Deep Learning Normal Distribution Proto-Oncogene Proteins p21(ras) Protein Binding
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