AIMC Topic: Coronavirus 3C Proteases

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Predicting cryptic ligand binding sites based on normal modes guided conformational sampling.

Proteins Dec 5, 2020
To greatly expand the druggable genome, fast and accurate predictions of cryptic sites for small molecules binding in target proteins are in high demand. In this study, we have developed a fast and simple conformational sampling scheme guided by norm...
Interleukin-2 Models, Statistical Regression Analysis Area Under Curve SARS-CoV-2 ROC Curve Computational Biology Antigens, Neoplasm Elasticity Protein Conformation Receptors, Cytoplasmic and Nuclear Binding Sites Antigens, CD Molecular Dynamics Simulation Hepacivirus Ligands Humans Machine Learning Algorithms Reproducibility of Results Protein Tyrosine Phosphatase, Non-Receptor Type 1 Exportin 1 Protein Coronavirus 3C Proteases Coronavirus Papain-Like Proteases Karyopherins
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Virtual screening of anti-HIV1 compounds against SARS-CoV-2: machine learning modeling, chemoinformatics and molecular dynamics simulation based analysis.

Scientific reports Nov 23, 2020
COVID-19 caused by the SARS-CoV-2 is a current global challenge and urgent discovery of potential drugs to combat this pandemic is a need of the hour. 3-chymotrypsin-like cysteine protease (3CLpro) enzyme is the vital molecular target against the SAR...
Humans COVID-19 SARS-CoV-2 Molecular Docking Simulation Deep Learning Protease Inhibitors Cheminformatics Coronavirus 3C Proteases Infectious bronchitis virus Molecular Dynamics Simulation Drug Evaluation, Preclinical HIV-1 COVID-19 Drug Treatment Anti-HIV Agents Antiviral Agents Drug Repositioning
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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...
Catalytic Domain Coronavirus 3C Proteases Coronavirus Protease Inhibitors Protein Binding Drug Repositioning Workflow Molecular Dynamics Simulation Neural Networks, Computer Drug Discovery Antiviral Agents
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Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization.

Journal of chemical information and modeling Sep 9, 2020
Artificial intelligence and multiobjective optimization represent promising solutions to bridge chemical and biological landscapes by addressing the automated design of compounds as a result of a humanlike creative process. In the present study, we ...
Acetylcholinesterase Cholinesterase Inhibitors Enzyme Inhibitors Neural Networks, Computer Viral Nonstructural Proteins Coronavirus 3C Proteases Artificial Intelligence Small Molecule Libraries Pandemics Cysteine Endopeptidases Influenza A virus COVID-19 Betacoronavirus Antiviral Agents Pneumonia, Viral Coronavirus Infections Humans Neuraminidase SARS-CoV-2 Molecular Docking Simulation Drug Design
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Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov.

Interdisciplinary sciences, computational life sciences Jun 1, 2020
A novel coronavirus, called 2019-nCoV, was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. Although there are some drugs to treat 2019-nCoV, there is no proper scientific evidence abou...
Sequence Alignment Cysteine Endopeptidases Databases, Pharmaceutical Structural Homology, Protein Oligopeptides Viral Nonstructural Proteins Databases, Nucleic Acid Betacoronavirus Antiviral Agents SARS-CoV-2 Pneumonia, Viral Models, Molecular Drug Design Coronavirus 3C Proteases Molecular Dynamics Simulation Deep Learning Amino Acid Sequence Drug Evaluation, Preclinical User-Computer Interface Humans Coronavirus Infections Pandemics Ligands COVID-19 Catalytic Domain
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A deep learning model for structure-based bioactivity optimization and its application in the bioactivity optimization of a SARS-CoV-2 main protease inhibitor.

European journal of medicinal chemistry Jul 5, 2025
Bioactivity optimization is a crucial and technical task in the early stages of drug discovery, traditionally carried out through iterative substituent optimization, a process that is often both time-consuming and expensive. To address this challenge...
Coronavirus 3C Proteases SARS-CoV-2 Drug Discovery Deep Learning Antiviral Agents Structure-Activity Relationship Molecular Structure COVID-19 Drug Treatment Humans Protease Inhibitors COVID-19
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Drug repurposing targeting COVID-19 3CL protease using molecular docking and machine learning regression approaches.

Scientific reports May 28, 2025
The COVID-19 pandemic has initiated a global health emergency, with an exigent need for an effective cure. Progressively, drug repurposing is emerging as a promising solution for saving time, cost, and labor. However, the number of drug candidates th...
COVID-19 SARS-CoV-2 Molecular Docking Simulation Antiviral Agents Humans Machine Learning Pandemics Viral Nonstructural Proteins Cysteine Endopeptidases Betacoronavirus Coronavirus 3C Proteases Protein Binding Drug Repositioning COVID-19 Drug Treatment Quantitative Structure-Activity Relationship
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