AIMC Topic: Molecular Docking Simulation

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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...
Betacoronavirus Humans Machine Learning SARS-CoV-2 Drug Evaluation, Preclinical Protein Conformation Molecular Docking Simulation Hydrogen Bonding Antiviral Agents Spike Glycoprotein, Coronavirus
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Predictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease.

Journal of biomolecular structure & dynamics Aug 5, 2020
The whole world is facing a great challenging time due to Coronavirus disease (COVID-19) caused by SARS-CoV-2. Globally, more than 14.6 M people have been diagnosed and more than 595 K deaths are reported. Currently, no effective vaccine or drugs are...
Molecular Dynamics Simulation Humans COVID-19 Protease Inhibitors SARS-CoV-2 Peptide Hydrolases Molecular Docking Simulation Deep Learning
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Molecular docking and machine learning analysis of Abemaciclib in colon cancer.

BMC molecular and cell biology Jul 8, 2020
BACKGROUND: The main challenge in cancer research is the identification of different omic variables that present a prognostic value and personalised diagnosis for each tumour. The fact that the diagnosis is personalised opens the doors to the design ...
Gene Expression Profiling Cell Line, Tumor Gene Expression Regulation, Neoplastic Algorithms Prognosis Molecular Docking Simulation Neoplasm Staging Colonic Neoplasms Survival Analysis Adenocarcinoma Databases, Protein Drug Repositioning Humans Machine Learning Gastrointestinal Hormones Benzimidazoles Epistasis, Genetic Aminopyridines Fatty Acid-Binding Proteins
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Insight into potent leads for alzheimer's disease by using several artificial intelligence algorithms.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie Jun 16, 2020
Several proteins including S-nitrosoglutathione reductase (GSNOR), complement Factor D, complement 3b (C3b) and Protein Kinase R-like Endoplasmic Reticulum Kinase (PERK), have been demonstrated to be involved in pathogenesis pathways for Alzheimer's ...
Alzheimer Disease Molecular Targeted Therapy Quantitative Structure-Activity Relationship Nootropic Agents Signal Transduction Molecular Structure Molecular Dynamics Simulation Plant Extracts Cognition Brain Computer-Aided Design Humans Animals Drug Design Molecular Docking Simulation Artificial Intelligence Drug Discovery
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A Deep-Learning Approach toward Rational Molecular Docking Protocol Selection.

Molecules (Basel, Switzerland) May 27, 2020
While a plethora of different protein-ligand docking protocols have been developed over the past twenty years, their performances greatly depend on the provided input protein-ligand pair. In this study, we developed a machine-learning model that uses...
Machine Learning Cheminformatics Molecular Docking Simulation Deep Learning Databases, Protein
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Using machine learning to improve ensemble docking for drug discovery.

Proteins May 25, 2020
Ensemble docking has provided an inexpensive method to account for receptor flexibility in molecular docking for virtual screening. Unfortunately, as there is no rigorous theory to connect the docking scores from multiple structures to measured activ...
Ligands ErbB Receptors Protein Kinase Inhibitors Binding Sites Protein Structure, Secondary Drug Discovery Humans User-Computer Interface Protein Binding Molecular Docking Simulation Support Vector Machine Bayes Theorem
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Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring.

Journal of chemical information and modeling May 11, 2020
Virtual Screening (VS) based on molecular docking is an efficient method used for retrieving novel hit compounds in drug discovery. However, the accuracy of the current docking scoring function (SF) is usually insufficient. In this study, in order to...
Machine Learning Ligands Molecular Docking Simulation Protein Binding Proteins
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Binding Affinity Prediction by Pairwise Function Based on Neural Network.

Journal of chemical information and modeling May 11, 2020
We present a new approach to estimate the binding affinity from given three-dimensional poses of protein-ligand complexes. In this scheme, every protein-ligand atom pair makes an additive free-energy contribution. The sum of these pairwise contributi...
Protein Binding Molecular Docking Simulation Neural Networks, Computer Ligands Drug Design
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Combined Machine Learning and Molecular Modelling Workflow for the Recognition of Potentially Novel Fungicides.

Molecules (Basel, Switzerland) May 8, 2020
Novel machine learning and molecular modelling filtering procedures for drug repurposing have been carried out for the recognition of the novel fungicide targets of Cyp51 and Erg2. Classification and regression approaches on molecular descriptors hav...
Software Fungicides, Industrial Machine Learning Molecular Docking Simulation Molecular Dynamics Simulation Workflow
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LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening.

Journal of chemical information and modeling Apr 23, 2020
Comparative evaluation of virtual screening methods requires a rigorous benchmarking procedure on diverse, realistic, and unbiased data sets. Recent investigations from numerous research groups unambiguously demonstrate that artificially constructed ...
Proteins Machine Learning Ligands Molecular Docking Simulation
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