AIMC Topic: Molecular Docking Simulation

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An in silico deep learning approach to multi-epitope vaccine design: a SARS-CoV-2 case study.

Scientific reports Feb 5, 2021
The rampant spread of COVID-19, an infectious disease caused by SARS-CoV-2, all over the world has led to over millions of deaths, and devastated the social, financial and political entities around the world. Without an existing effective medical the...
Humans COVID-19 SARS-CoV-2 Epitopes, T-Lymphocyte Molecular Docking Simulation T-Lymphocytes, Cytotoxic Codon Usage Molecular Dynamics Simulation Allergens Solubility Immunogenicity, Vaccine T-Lymphocytes, Helper-Inducer Protein Conformation Epitopes, B-Lymphocyte Vaccines, Subunit Computational Biology Models, Molecular Drug Design Mutation Deep Learning RNA, Viral COVID-19 Vaccines Spike Glycoprotein, Coronavirus
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Predicting Potential SARS-COV-2 Drugs-In Depth Drug Database Screening Using Deep Neural Network Framework SSnet, Classical Virtual Screening and Docking.

International journal of molecular sciences Feb 4, 2021
Severe Acute Respiratory Syndrome Corona Virus 2 has altered life on a global scale. A concerted effort from research labs around the world resulted in the identification of potential pharmaceutical treatments for CoVID-19 using existing drugs, as we...
Drug Discovery Antiviral Agents Spike Glycoprotein, Coronavirus Drug Repositioning COVID-19 Algorithms SARS-CoV-2 Molecular Docking Simulation Drug Evaluation, Preclinical COVID-19 Drug Treatment Angiotensin-Converting Enzyme 2 Databases, Pharmaceutical Humans Neural Networks, Computer Machine Learning
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New machine learning and physics-based scoring functions for drug discovery.

Scientific reports Feb 4, 2021
Scoring functions are essential for modern in silico drug discovery. However, the accurate prediction of binding affinity by scoring functions remains a challenging task. The performance of scoring functions is very heterogeneous across different tar...
Research Design Molecular Docking Simulation Drug Discovery Support Vector Machine Protease Inhibitors Humans Internet Entropy Peptide Hydrolases Software Ligands Protein Interaction Mapping Hydrophobic and Hydrophilic Interactions Drugs, Investigational Datasets as Topic
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Hg(II) sensing, catalytic, antioxidant, antimicrobial, and anticancer potential of Garcinia mangostana and α-mangostin mediated silver nanoparticles.

Chemosphere Jan 28, 2021
This study reports synthesis of Garcinia mangostana fruit pericarp (unwanted waste material) and α-mangostin mediated silver nanoparticles (AgNPs). These AgNPs were efficiently produced using 1:10 (extract and salt) ratio under stirring and heating, ...
Garcinia mangostana Mercury Anti-Bacterial Agents Plant Extracts Xanthones Metal Nanoparticles Silver Anti-Infective Agents Coloring Agents Molecular Docking Simulation Antioxidants
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Classification and prediction of protein-protein interaction interface using machine learning algorithm.

Scientific reports Jan 19, 2021
Structural insight of the protein-protein interaction (PPI) interface can provide knowledge about the kinetics, thermodynamics and molecular functions of the complex while elucidating its role in diseases and further enabling it as a potential therap...
Databases, Protein Models, Molecular Binding Sites Thermodynamics Protein Interaction Mapping Protein Interaction Maps Protein Binding Support Vector Machine Proteins Molecular Docking Simulation
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Repurposing potential of FDA-approved and investigational drugs for COVID-19 targeting SARS-CoV-2 spike and main protease and validation by machine learning algorithm.

Chemical biology & drug design Dec 22, 2020
The present study aimed to assess the repurposing potential of existing antiviral drug candidates (FDA-approved and investigational) against SARS-CoV-2 target proteins that facilitates viral entry and replication into the host body. To evaluate molec...
Protease Inhibitors Deoxyadenosines Viral Matrix Proteins Molecular Docking Simulation Antiviral Agents Spike Glycoprotein, Coronavirus Humans Cell Line Machine Learning Structure-Activity Relationship COVID-19 Cell Survival COVID-19 Drug Treatment SARS-CoV-2 Drug Repositioning Binding Sites
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Target-Specific Drug Design Method Combining Deep Learning and Water Pharmacophore.

Journal of chemical information and modeling Nov 30, 2020
Following identification of a target protein, hit identification, which finds small organic molecules that bind to the target, is an important first step of a structure-based drug design project. In this study, we demonstrate a target-specific drug d...
Algorithms Proteins Molecular Docking Simulation Ligands Drug Design Deep Learning Water
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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...
COVID-19 Drug Treatment Protease Inhibitors Cheminformatics Coronavirus 3C Proteases Infectious bronchitis virus Humans Drug Repositioning Molecular Dynamics Simulation COVID-19 Drug Evaluation, Preclinical SARS-CoV-2 HIV-1 Molecular Docking Simulation Deep Learning Anti-HIV Agents Antiviral Agents
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Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations.

Journal of chemical information and modeling Nov 16, 2020
Drug-induced cardiotoxicity is a potentially lethal and yet one of the most common side effects with the drugs in clinical use. Most of the drug-induced cardiotoxicity is associated with an off-target pharmacological blockade of K currents carried ou...
Humans Machine Learning Molecular Docking Simulation Models, Molecular Bayes Theorem Ligands Ether-A-Go-Go Potassium Channels
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Repurposing therapeutics for COVID-19: Rapid prediction of commercially available drugs through machine learning and docking.

PloS one Nov 12, 2020
BACKGROUND: The outbreak of the novel coronavirus disease COVID-19, caused by the SARS-CoV-2 virus has spread rapidly around the globe during the past 3 months. As the virus infected cases and mortality rate of this disease is increasing exponentiall...
Coronavirus Infections Betacoronavirus Humans SARS-CoV-2 Pneumonia, Viral Molecular Docking Simulation Machine Learning Drug Repositioning Pandemics Bayes Theorem COVID-19 Algorithms
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