AI Medical Compendium Topic:
Protein Binding

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AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks.

International journal of molecular sciences Nov 10, 2020
Accurate prediction of the binding affinity of a protein-ligand complex is essential for efficient and successful rational drug design. Therefore, many binding affinity prediction methods have been developed. In recent years, since deep learning tech...
Drug Design Drug Discovery Deep Learning Neural Networks, Computer Molecular Docking Simulation Computer-Aided Design Databases, Protein Molecular Dynamics Simulation Ligands User-Computer Interface Protein Binding Proteins Humans
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Profiling SARS-CoV-2 Main Protease (M) Binding to Repurposed Drugs Using Molecular Dynamics Simulations in Classical and Neural Network-Trained Force Fields.

ACS combinatorial science Oct 29, 2020
The current COVID-19 pandemic caused by a novel coronavirus SARS-CoV-2 urgently calls for a working therapeutic. Here, we report a computation-based workflow for efficiently selecting a subset of FDA-approved drugs that can potentially bind to the SA...
Neural Networks, Computer Drug Discovery Coronavirus 3C Proteases Coronavirus Protease Inhibitors Workflow Antiviral Agents Molecular Dynamics Simulation Protein Binding Catalytic Domain Drug Repositioning
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Spatiotemporal identification of druggable binding sites using deep learning.

Communications biology Oct 27, 2020
Identification of novel protein binding sites expands druggable genome and opens new opportunities for drug discovery. Generally, presence or absence of a binding site depends on the three-dimensional conformation of a protein, making binding site id...
Binding Sites Ion Channel Gating Receptors, Purinergic P2X3 Models, Biological Adenosine Triphosphate Protein Conformation Receptors, G-Protein-Coupled Models, Molecular Software Drug Delivery Systems Deep Learning Protein Binding
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Performance of Force-Field- and Machine Learning-Based Scoring Functions in Ranking MAO-B Protein-Inhibitor Complexes in Relevance to Developing Parkinson's Therapeutics.

International journal of molecular sciences Oct 16, 2020
Monoamine oxidase B (MAOB) is expressed in the mitochondrial membrane and has a key role in degrading various neurologically active amines such as benzylamine, phenethylamine and dopamine with the help of Flavin adenine dinucleotide (FAD) cofactor. T...
Humans Machine Learning Molecular Docking Simulation Antiparkinson Agents Monoamine Oxidase Inhibitors Protein Binding Drug Development Monoamine Oxidase
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Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks.

Journal of chemical information and modeling Oct 14, 2020
The high-performance computational techniques have brought significant benefits for drug discovery efforts in recent decades. One of the most challenging problems in drug discovery is the protein-ligand binding pose prediction. To predict the most st...
Protein Binding Proteins Ligands Neural Networks, Computer Software Molecular Docking Simulation
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SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features.

International journal of molecular sciences Oct 1, 2020
Protein Hot-Spots (HS) are experimentally determined amino acids, key to small ligand binding and tend to be structural landmarks on protein-protein interactions. As such, they were extensively approached by structure-based Machine Learning (ML) pred...
Humans Amino Acids Amino Acid Sequence Datasets as Topic Binding Sites Protein Interaction Mapping Computational Biology Proteins Machine Learning Databases, Protein Protein Binding
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Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening.

Journal of chemical information and modeling Sep 16, 2020
Docking is one of the most important steps in virtual screening pipelines, and it is an established method for examining potential interactions between ligands and receptors. However, this method is computationally expensive, and it is often among th...
Receptors, G-Protein-Coupled Ligands Molecular Docking Simulation Protein Binding Neural Networks, Computer Software Retrospective Studies
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iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network.

Journal of molecular biology Sep 11, 2020
DNA-binding protein (DBP) and RNA-binding protein (RBP) are playing crucial roles in gene expression. Accurate identification of them is of great significance, and accurately computational predictors are highly required. In previous studies, DBP reco...
RNA-Binding Proteins Machine Learning Humans DNA-Binding Proteins Protein Binding RNA Binding Sites Neural Networks, Computer Computational Biology
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Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks.

Cell systems Sep 10, 2020
Epidemiological studies show that SARS-CoV-2 infection leads to severe symptoms only in a fraction of patients, but the determinants of individual susceptibility to the virus are still unknown. The major histocompatibility complex (MHC) class I expos...
Protein Binding Histocompatibility Antigens Class I Humans Haplotypes Neural Networks, Computer SARS-CoV-2 Peptides Polymorphism, Genetic Viral Proteins Betacoronavirus
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Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design.

Journal of chemical information and modeling Sep 10, 2020
One of the main challenges in drug discovery is predicting protein-ligand binding affinity. Recently, machine learning approaches have made substantial progress on this task. However, current methods of model evaluation are overly optimistic in measu...
Drug Design Neural Networks, Computer Ligands Protein Binding Databases, Protein
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