AIMC Topic: Protein Conformation

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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 Regulation Receptors, Adrenergic, beta-2 Allosteric Site Humans Molecular Dynamics Simulation Drug Design Machine Learning Protein Conformation
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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...
Deep Learning Bacillus subtilis Mass Spectrometry Bacterial Proteins Protein Conformation Cross-Linking Reagents Models, Molecular Iron
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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...
Magnetic Resonance Spectroscopy Cryoelectron Microscopy Machine Learning Proteins Protein Conformation Nuclear Magnetic Resonance, Biomolecular Molecular Dynamics Simulation 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...
Protein Conformation Proteins Ligands Molecular Docking Simulation Protein Binding Machine Learning Software
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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...
Deep Learning Neural Networks, Computer Proteins Sequence Analysis, Protein Computational Biology Databases, Protein Algorithms Protein Conformation
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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...
Protein Conformation Normal Distribution Proto-Oncogene Proteins p21(ras) Humans Mutation Protein Binding Deep Learning Molecular Dynamics Simulation Principal Component Analysis
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Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure.

Journal of chemical information and modeling Aug 28, 2024
We present a computational scheme for predicting the ligands that bind to a pocket of a known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations, and permutati...
Small Molecule Libraries Protein Conformation Binding Sites Molecular Structure Ligands Protein Binding Machine Learning Proteins Algorithms Models, Molecular
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An end-to-end framework for the prediction of protein structure and fitness from single sequence.

Nature communications Aug 27, 2024
Significant research progress has been made in the field of protein structure and fitness prediction. Particularly, single-sequence-based structure prediction methods like ESMFold and OmegaFold achieve a balance between inference speed and prediction...
Neural Networks, Computer Computational Biology Proteins Algorithms Protein Stability Models, Molecular Protein Conformation Mutation Sequence Analysis, Protein
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