AIMC Topic: Molecular Dynamics Simulation

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Artificial intelligence assisted identification of potential tau aggregation inhibitors: ligand- and structure-based virtual screening, in silico ADME, and molecular dynamics study.

Molecular diversity
Alzheimer's disease (AD) is a severe, growing, multifactorial disorder affecting millions of people worldwide characterized by cognitive decline and neurodegeneration. The accumulation of tau protein into paired helical filaments is one of the major ...

Identification of medicinal plant-based phytochemicals as a potential inhibitor for SARS-CoV-2 main protease (M) using molecular docking and deep learning methods.

Computers in biology and medicine
Highly transmissive and rapidly evolving Coronavirus disease-2019 (COVID-19), a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), triggered a global pandemic, which is one of the most researched viruses in the acad...

Uncertainty-driven dynamics for active learning of interatomic potentials.

Nature computational science
Machine learning (ML) models, if trained to data sets of high-fidelity quantum simulations, produce accurate and efficient interatomic potentials. Active learning (AL) is a powerful tool to iteratively generate diverse data sets. In this approach, th...

Protein Design Using Physics Informed Neural Networks.

Biomolecules
The inverse protein folding problem, also known as protein sequence design, seeks to predict an amino acid sequence that folds into a specific structure and performs a specific function. Recent advancements in machine learning techniques have been su...

Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds.

Molecular diversity
To date, the COVID-19 pandemic has still been infectious around the world, continuously causing social and economic damage on a global scale. One of the most important therapeutic targets for the treatment of COVID-19 is the main protease (Mpro) of S...

Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches.

Journal of chemical information and modeling
Allosteric mechanisms are commonly employed regulatory tools used by proteins to orchestrate complex biochemical processes and control communications in cells. The quantitative understanding and characterization of allosteric molecular events are amo...

Optimizing variant-specific therapeutic SARS-CoV-2 decoys using deep-learning-guided molecular dynamics simulations.

Scientific reports
Treatment of COVID-19 with a soluble version of ACE2 that binds to SARS-CoV-2 virions before they enter host cells is a promising approach, however it needs to be optimized and adapted to emerging viral variants. The computational workflow presented ...

Machine Learning Assisted Clustering of Nanoparticle Structures.

Journal of chemical information and modeling
We propose a scheme for the automatic separation (i.e., clustering) of data sets composed of several nanoparticle (NP) structures by means of Machine Learning techniques. These data sets originate from atomistic simulations, such as global optimizati...

Prediction of Kinetic Product Ratios: Investigation of a Dynamically Controlled Case.

The journal of physical chemistry. A
Of the various factors influencing kinetically controlled product ratios, the role of nonstatistical dynamics is arguably the least well understood. In this paper, reactions were chosen in which dynamics played a dominant role in product selection, b...

Computational Biomaterials: Computational Simulations for Biomedicine.

Advanced materials (Deerfield Beach, Fla.)
With the flourishing development of material simulation methods (quantum chemistry methods, molecular dynamics, Monte Carlo, phase field, etc.), extensive adoption of computing technologies (high-throughput, artificial intelligence, machine learning,...