AIMC Topic: Protein Conformation

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Conformational changes of β-thalassemia major hemoglobin and oxidative status of plasma after in vitro exposure to extremely low-frequency electromagnetic fields: An artificial neural network analysis.

Electromagnetic biology and medicine Oct 23, 2020
Electromagnetic fields (EMF) can generate reactive oxygen species and induce oxidative modifications. We investigated the effects of extremely low-frequency electromagnetic fields (ELF-EMF) on oxidative status of plasma and erythrocytes in β-thalasse...
Humans Neural Networks, Computer Oxidative Stress beta-Thalassemia Protein Conformation Electromagnetic Fields Oxidation-Reduction Hemoglobins
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Characterizing chromatin folding coordinate and landscape with deep learning.

PLoS computational biology Sep 28, 2020
Genome organization is critical for setting up the spatial environment of gene transcription, and substantial progress has been made towards its high-resolution characterization. The underlying molecular mechanism for its establishment is much less u...
Computer Simulation Deep Learning Thermodynamics Models, Biological Histone Code Genome Protein Conformation Chromatin
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Discovering Protein Conformational Flexibility through Artificial-Intelligence-Aided Molecular Dynamics.

The journal of physical chemistry. B Sep 9, 2020
Proteins sample a variety of conformations distinct from their crystal structure. These structures, their propensities, and the pathways for moving between them contain an enormous amount of information about protein function that is hidden from a pu...
Molecular Dynamics Simulation Protein Conformation Humans Proteins Intelligence Artificial Intelligence
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Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies.

The journal of physical chemistry letters Aug 14, 2020
The current pandemic demands a search for therapeutic agents against the novel coronavirus SARS-CoV-2. Here, we present an efficient computational strategy that combines machine learning (ML)-based models and high-fidelity ensemble docking studies to...
Antiviral Agents Spike Glycoprotein, Coronavirus Drug Evaluation, Preclinical SARS-CoV-2 Molecular Docking Simulation Betacoronavirus Protein Conformation Hydrogen Bonding Humans Machine Learning
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Predicting protein model correctness in Coot using machine learning.

Acta crystallographica. Section D, Structural biology Jul 27, 2020
Manually identifying and correcting errors in protein models can be a slow process, but improvements in validation tools and automated model-building software can contribute to reducing this burden. This article presents a new correctness score that ...
Models, Molecular Crystallography, X-Ray Protein Conformation Software Proteins Machine Learning
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Anomaly Detection-Based Recognition of Near-Native Protein Structures.

IEEE transactions on nanobioscience Apr 27, 2020
The three-dimensional structures populated by a protein molecule determine to a great extent its biological activities. The rich information encoded by protein structure on protein function continues to motivate the development of computational appro...
Protein Conformation Machine Learning Algorithms Proteins Databases, Protein Computational Biology
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Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains.

Journal of chemical theory and computation Apr 7, 2020
Understanding the conformational characteristics of protein complexes in solution is crucial for a deeper insight in their biological function. Molecular dynamics simulations performed on high performance computing plants and with modern simulation t...
Ubiquitin Machine Learning Molecular Dynamics Simulation Protein Conformation
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Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials.

Journal of chemical information and modeling Mar 30, 2020
Despite significant advances in resolution, the potential for cryo-electron microscopy (EM) to be used in determining the structures of protein-drug complexes remains unrealized. Determination of accurate structures and coordination of bound ligands ...
Protein Conformation Neural Networks, Computer Cryoelectron Microscopy Molecular Dynamics Simulation Molecular Conformation Microscopy, Electron
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Big data and artificial intelligence discover novel drugs targeting proteins without 3D structure and overcome the undruggable targets.

Stroke and vascular neurology Mar 29, 2020
The discovery of targeted drugs heavily relies on three-dimensional (3D) structures of target proteins. When the 3D structure of a protein target is unknown, it is very difficult to design its corresponding targeted drugs. Although the 3D structures ...
Big Data Proteins Structure-Activity Relationship Molecular Structure Databases, Protein Drug Design Drug Discovery Animals Computer-Aided Design Humans Ligands Pharmaceutical Preparations Artificial Intelligence Data Mining Molecular Targeted Therapy Protein Conformation
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IMPContact: An Interhelical Residue Contact Prediction Method.

BioMed research international Mar 25, 2020
As an important category of proteins, alpha-helix transmembrane proteins (TMPs) play an important role in various biological activities. Because the solved αTMP structures are inadequate, predicting the residue contacts among the transmembrane segmen...
Membrane Proteins Databases, Protein Algorithms Neural Networks, Computer Protein Conformation Computational Biology Machine Learning
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