Molecular Dynamics Simulation

Unveiling G-protein coupled receptor kinase-5 inhibitors for chronic degenerative diseases: Multilayered prioritization employing explainable machine learning-driven multi-class QSAR, ligand-based pharmacophore and free energy-inspired molecular simulation.

International journal of biological macromolecules Apr 30, 2024

GRK5 holds a pivotal role in cellular signaling pathways, with its overexpression in cardiomyocytes, neuronal cells, and tumor cells strongly associated with various chronic degenerative diseases, which highlights the urgent need for potential inhibi...

Chronic Disease Molecular Dynamics Simulation Ligands Molecular Docking Simulation Protein Binding Thermodynamics Pharmacophore G-Protein-Coupled Receptor Kinase 5 Quantitative Structure-Activity Relationship Protein Kinase Inhibitors Binding Sites Humans Machine Learning

View on PubMed DOI

Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning.

Journal of chemical information and modeling Apr 30, 2024

L2 β-lactamases, serine-based class A β-lactamases expressed by , play a pivotal role in antimicrobial resistance (AMR). However, limited studies have been conducted on these important enzymes. To understand the coevolutionary dynamics of L2 β-lactam...

Deep Learning Evolution, Molecular Molecular Dynamics Simulation Protein Conformation beta-Lactamases Stenotrophomonas maltophilia

View on PubMed DOI

Exploring Antiviral Drugs on Monolayer Black Phosphorene: Atomistic Theory and Explainable Machine Learning-Assisted Platform.

International journal of molecular sciences Apr 30, 2024

Favipiravir (FP) and ebselen (EB) belong to a diverse class of antiviral drugs known for their significant efficacy in treating various viral infections. Utilizing molecular dynamics (MD) simulations, machine learning, and van der Waals density funct...

Isoindoles Organoselenium Compounds Thermodynamics Density Functional Theory Machine Learning Azoles Antiviral Agents Molecular Dynamics Simulation

View on PubMed DOI

Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning.

The journal of physical chemistry. A Apr 29, 2024

Solvatochromism occurs in both homogeneous solvents and more complex biological environments, such as proteins. While in both cases the solvatochromic effects report on the surroundings of the chromophore, their interpretation in proteins becomes mor...

Machine Learning Solvents Proteins Molecular Dynamics Simulation Quantum Theory Carotenoids

View on PubMed DOI

Predicting FFAR4 agonists using structure-based machine learning approach based on molecular fingerprints.

Scientific reports Apr 24, 2024

Free Fatty Acid Receptor 4 (FFAR4), a G-protein-coupled receptor, is responsible for triggering intracellular signaling pathways that regulate various physiological processes. FFAR4 agonists are associated with enhancing insulin release and mitigatin...

Molecular Dynamics Simulation Ligands Binding Sites Receptors, G-Protein-Coupled Bayes Theorem Humans Machine Learning Molecular Docking Simulation Protein Binding

View on PubMed DOI

HBCVTr: an end-to-end transformer with a deep neural network hybrid model for anti-HBV and HCV activity predictor from SMILES.

Scientific reports Apr 22, 2024

Hepatitis B and C viruses (HBV and HCV) are significant causes of chronic liver diseases, with approximately 350 million infections globally. To accelerate the finding of effective treatment options, we introduce HBCVTr, a novel ligand-based drug des...

Molecular Dynamics Simulation Hepacivirus Hepatitis C Hepatitis B virus Hepatitis B Ligands Viral Nonstructural Proteins Humans Neural Networks, Computer Molecular Docking Simulation Drug Design Antiviral Agents

View on PubMed DOI

Differentiating stable and unstable protein using convolution neural network and molecular dynamics simulations.

Computational biology and chemistry Apr 20, 2024

Protein stability is a critical aspect of molecular biology and biochemistry, hinges on an intricate balance of thermodynamic and structural factors. Determining protein stability is crucial for understanding and manipulating biological machineries, ...

Molecular Dynamics Simulation Neural Networks, Computer Protein Stability Thermodynamics Machine Learning Proteins

View on PubMed DOI

Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning.

Molecules (Basel, Switzerland) Apr 19, 2024

Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calcula...

Humans Molecular Docking Simulation Deep Learning Protein Binding Nuclear Proteins Transcription Factors Azepines Cell Cycle Proteins Molecular Dynamics Simulation Bromodomain Containing Proteins Binding Sites Triazoles Thermodynamics

View on PubMed DOI

How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided enhanced sampling algorithms.

Current opinion in structural biology Apr 16, 2024

Molecular simulations are an essential asset in the first steps of drug design campaigns. However, the requirement of high-throughput limits applications mainly to qualitative approaches with low computational cost, but also low accuracy. Unlocking t...

Algorithms Drug Design Molecular Dynamics Simulation Machine Learning Quantum Theory

View on PubMed DOI

Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning.

Journal of chemical information and modeling Apr 16, 2024

Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical m...

Amino Acids Thermodynamics Molecular Dynamics Simulation Neural Networks, Computer Machine Learning Nanostructures Algorithms Adsorption

View on PubMed DOI

AI Medical Compendium Topic

Explore the latest research on artificial intelligence and machine learning in medicine.

Unveiling G-protein coupled receptor kinase-5 inhibitors for chronic degenerative diseases: Multilayered prioritization employing explainable machine learning-driven multi-class QSAR, ligand-based pharmacophore and free energy-inspired molecular simulation.

Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning.

Exploring Antiviral Drugs on Monolayer Black Phosphorene: Atomistic Theory and Explainable Machine Learning-Assisted Platform.

Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning.

Predicting FFAR4 agonists using structure-based machine learning approach based on molecular fingerprints.

HBCVTr: an end-to-end transformer with a deep neural network hybrid model for anti-HBV and HCV activity predictor from SMILES.

Differentiating stable and unstable protein using convolution neural network and molecular dynamics simulations.

Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning.

How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided enhanced sampling algorithms.

Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning.

Popular Topics

Recent Journals