AIMC Topic: Molecular Dynamics Simulation

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Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks.

Journal of chemical theory and computation Mar 29, 2021
Several experimental studies indicated that large conformational changes, including partial domain unfolding, have a role in the functional mechanisms of the basic helix loop helix Per/ARNT/SIM (bHLH-PAS) transcription factors. Recently, single-molec...
Protein Unfolding Basic Helix-Loop-Helix Transcription Factors Molecular Dynamics Simulation Microscopy, Atomic Force Protein Conformation Neural Networks, Computer
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Characterizing the function of domain linkers in regulating the dynamics of multi-domain fusion proteins by microsecond molecular dynamics simulations and artificial intelligence.

Proteins Mar 27, 2021
Multi-domain proteins are not only formed through natural evolution but can also be generated by recombinant DNA technology. Because many fusion proteins can enhance the selectivity of cell targeting, these artificially produced molecules, called mul...
Recombinant Fusion Proteins Protein Engineering Pliability Mutagenesis, Insertional Amino Acids Benchmarking Molecular Dynamics Simulation Artificial Intelligence Computational Biology Gene Expression Protein Domains Humans
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Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with a Machine Learning Model.

Journal of chemical information and modeling Mar 17, 2021
The molecular dynamics (MD) simulation technique is among the most broadly used computational methods to investigate atomistic phenomena in a variety of chemical and biological systems. One of the most common (and most uncertain) parametrization step...
Machine Learning Molecular Dynamics Simulation Uncertainty Solvents Static Electricity
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Target2DeNovoDrug: a novel programmatic tool for -deep learning based drug design for any target of interest.

Journal of biomolecular structure & dynamics Mar 11, 2021
The on-going data-science and Artificial Intelligence (AI) revolution offer researchers a fresh set of tools to approach structure-based drug design problems in the computer-aided drug design space. A novel programmatic tool that incorporates and de...
Deep Learning Molecular Dynamics Simulation Ligands Artificial Intelligence Drug Design
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Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations.

Nature biomedical engineering Mar 11, 2021
The de novo design of antimicrobial therapeutics involves the exploration of a vast chemical repertoire to find compounds with broad-spectrum potency and low toxicity. Here, we report an efficient computational method for the generation of antimicrob...
Pseudomonas aeruginosa Acinetobacter baumannii Structure-Activity Relationship Molecular Dynamics Simulation Amino Acid Sequence Drug Design Drug Discovery Deep Learning Microbial Sensitivity Tests Drug Resistance, Bacterial Female Animals Anti-Bacterial Agents Mice, Inbred BALB C Antimicrobial Cationic Peptides Escherichia coli Staphylococcus aureus Mice Klebsiella pneumoniae Klebsiella Infections
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A novel artificial intelligence protocol to investigate potential leads for diabetes mellitus.

Molecular diversity Mar 9, 2021
Dipeptidyl peptidase-4 (DPP4) is highly participated in regulating diabetes mellitus (DM), and inhibitors of DPP4 may act as potential DM drugs. Therefore, we performed a novel artificial intelligence (AI) protocol to screen and validate the potentia...
Humans Neural Networks, Computer Artificial Intelligence Machine Learning Workflow Molecular Dynamics Simulation Drug Discovery Quantitative Structure-Activity Relationship Dipeptidyl-Peptidase IV Inhibitors Algorithms Protein Binding Hydrogen Bonding Molecular Docking Simulation Hypoglycemic Agents Binding Sites Drug Design Molecular Structure
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MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes.

Journal of computational chemistry Mar 6, 2021
Machine Learning-assisted Lipid Phase Analysis (MLLPA) is a new Python 3 module developed to analyze phase domains in a lipid membrane based on lipid molecular states. Reading standard simulation coordinate and trajectory files, the software first an...
Molecular Dynamics Simulation Membrane Lipids Machine Learning
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In silico design of novel aptamers utilizing a hybrid method of machine learning and genetic algorithm.

Molecular diversity Feb 7, 2021
Aptamers can be regarded as efficient substitutes for monoclonal antibodies in many diagnostic and therapeutic applications. Due to the tedious and prohibitive nature of SELEX (systematic evolution of ligands by exponential enrichment), the in silico...
Machine Learning RNA Aptamers, Nucleotide Molecular Docking Simulation Ligands Proteins Drug Design Molecular Dynamics Simulation Molecular Conformation Algorithms Biomarkers CD13 Antigens
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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...
Allergens Solubility Immunogenicity, Vaccine Epitopes, B-Lymphocyte Vaccines, Subunit T-Lymphocytes, Helper-Inducer Protein Conformation Models, Molecular Mutation RNA, Viral Molecular Dynamics Simulation COVID-19 Vaccines Spike Glycoprotein, Coronavirus Computational Biology T-Lymphocytes, Cytotoxic Codon Usage Epitopes, T-Lymphocyte Molecular Docking Simulation Drug Design Humans Deep Learning COVID-19 SARS-CoV-2
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Bringing Structural Implications and Deep Learning-Based Drug Identification for Mutants.

Journal of chemical information and modeling Jan 29, 2021
Colorectal cancer is considered one of the leading causes of death that is linked with the Kirsten Rat Sarcoma () harboring codons 13 and 61 mutations. The objective for this study is to search for clinically important codon 61 mutations and analyze ...
Codon Proto-Oncogene Proteins p21(ras) Humans Colorectal Neoplasms Deep Learning Mutation Pharmaceutical Preparations Molecular Dynamics Simulation
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