AIMC Topic: Molecular Dynamics Simulation

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A Machine Learning Approach to Identify Key Residues Involved in Protein-Protein Interactions Exemplified with SARS-CoV-2 Variants.

International journal of molecular sciences Jun 13, 2024
Human infection with the coronavirus disease 2019 (COVID-19) is mediated by the binding of the spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the human angiotensin-converting enzyme 2 (ACE2). The frequent mutatio...
Protein Binding Spike Glycoprotein, Coronavirus Mutation Molecular Dynamics Simulation Angiotensin-Converting Enzyme 2 Binding Sites Protein Interaction Domains and Motifs Machine Learning COVID-19 Humans SARS-CoV-2
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Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design.

Journal of chemical information and modeling Jun 6, 2024
Determining the viability of a new drug molecule is a time- and resource-intensive task that makes computer-aided assessments a vital approach to rapid drug discovery. Here we develop a machine learning algorithm, iMiner, that generates novel inhibit...
Machine Learning Algorithms Molecular Docking Simulation Artificial Intelligence Molecular Dynamics Simulation Drug Design Data Mining Proteins Ligands
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Screening structure and predicting toxicity of pesticide adjuvants using molecular dynamics simulation and machine learning for minimizing environmental impacts.

The Science of the total environment Jun 6, 2024
Surfactants as synergistic agents are necessary to improve the stability and utilization of pesticides, while their use is often accompanied by unexpected release into the environment. However, there are no efficient strategies available for screenin...
Surface-Active Agents Molecular Dynamics Simulation Zebrafish Animals Water Pollutants, Chemical Pesticides Octoxynol Machine Learning
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Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials.

Molecules (Basel, Switzerland) Jun 6, 2024
Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine...
Guanine Base Pairing Thermodynamics Protons Thymine DNA Molecular Dynamics Simulation Quantum Theory Machine Learning
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Application of molecular dynamics-based pharmacophore and machine learning approaches to identify novel Mcl1 inhibitors through drug repurposing and mechanics research.

Physical chemistry chemical physics : PCCP Jun 6, 2024
Myeloid cell leukemia 1 (Mcl1), a critical protein that regulates apoptosis, has been considered as a promising target for antitumor drugs. The conventional pharmacophore screening approach has limitations in conformation sampling and data mining. He...
Machine Learning Antineoplastic Agents Cell Line, Tumor Humans Fluvastatin Myeloid Cell Leukemia Sequence 1 Protein Pharmacophore Drug Repositioning Molecular Dynamics Simulation Quantum Theory
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Unveiling Conformational States of CDK6 Caused by Binding of Vcyclin Protein and Inhibitor by Combining Gaussian Accelerated Molecular Dynamics and Deep Learning.

Molecules (Basel, Switzerland) Jun 5, 2024
CDK6 plays a key role in the regulation of the cell cycle and is considered a crucial target for cancer therapy. In this work, conformational transitions of CDK6 were identified by using Gaussian accelerated molecular dynamics (GaMD), deep learning (...
Protein Kinase Inhibitors Binding Sites Thermodynamics Normal Distribution Cyclin-Dependent Kinase 6 Principal Component Analysis Molecular Dynamics Simulation Protein Conformation Deep Learning Protein Binding Humans
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Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities.

Journal of chemical information and modeling Jun 3, 2024
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can n...
Neural Networks, Computer Machine Learning Peptides Spectrum Analysis, Raman Molecular Dynamics Simulation Density Functional Theory Amino Acids
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NPEX: Never give up protein exploration with deep reinforcement learning.

Journal of molecular graphics & modelling May 25, 2024
Elucidating unknown structures of proteins, such as metastable states, is critical in designing therapeutic agents. Protein structure exploration has been performed using advanced computational methods, especially molecular dynamics and Markov chain ...
Dipeptides Proteins Protein Conformation Molecular Dynamics Simulation Monte Carlo Method Algorithms Markov Chains Deep Learning
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Impact of quantum and neuromorphic computing on biomolecular simulations: Current status and perspectives.

Current opinion in structural biology May 24, 2024
New high-performance computing architectures are becoming operative, in addition to exascale computers. Quantum computers (QC) solve optimization problems with unprecedented efficiency and speed, while neuromorphic hardware (NMH) simulates neural net...
Molecular Dynamics Simulation Quantum Theory Software Algorithms Neural Networks, Computer Machine Learning
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Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning.

Nature communications May 16, 2024
Biomacromolecule structures are essential for drug development and biocatalysis. Quantum refinement (QR) methods, which employ reliable quantum mechanics (QM) methods in crystallographic refinement, showed promise in improving the structural quality ...
Coronavirus 3C Proteases Humans Molecular Dynamics Simulation Quantum Theory COVID-19 Drug Treatment Machine Learning SARS-CoV-2 Antiviral Agents
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