AIMC Topic: Molecular Dynamics Simulation

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Virtual Screening of Small Molecules Targeting BCL2 with Machine Learning, Molecular Docking, and MD Simulation.

Biomolecules May 1, 2024
This study aimed to identify potential BCL-2 small molecule inhibitors using deep neural networks (DNN) and random forest (RF), algorithms as well as molecular docking and molecular dynamics (MD) simulations to screen a library of small molecules. Th...
Molecular Docking Simulation Protein Binding Molecular Dynamics Simulation Humans Machine Learning Proto-Oncogene Proteins c-bcl-2 Small Molecule Libraries
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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...
Pharmacophore G-Protein-Coupled Receptor Kinase 5 Binding Sites Thermodynamics Protein Binding Ligands Humans Quantitative Structure-Activity Relationship Chronic Disease Machine Learning Protein Kinase Inhibitors Molecular Docking Simulation Molecular Dynamics Simulation
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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...
Molecular Dynamics Simulation Deep Learning Protein Conformation beta-Lactamases Evolution, Molecular Stenotrophomonas maltophilia
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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 Density Functional Theory Thermodynamics Azoles Machine Learning Molecular Dynamics Simulation Antiviral Agents
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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 Carotenoids Proteins Molecular Dynamics Simulation Quantum Theory
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Integrated machine learning-based virtual screening and biological evaluation for identification of potential inhibitors against cathepsin K.

Molecular diversity Apr 25, 2024
Cathepsin K is a type of cysteine proteinase that is primarily expressed in osteoclasts and has a key role in the breakdown of bone matrix protein during bone resorption. Many studies suggest that the deficiency of cathepsin K is concomitant with a s...
Humans Drug Evaluation, Preclinical Machine Learning Cathepsin K Molecular Docking Simulation Cysteine Proteinase Inhibitors Molecular Dynamics Simulation
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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
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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...
Hepacivirus Hepatitis C Ligands Hepatitis B Molecular Dynamics Simulation Viral Nonstructural Proteins Humans Neural Networks, Computer Molecular Docking Simulation Drug Design Antiviral Agents Hepatitis B virus
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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, ...
Neural Networks, Computer Molecular Dynamics Simulation Protein Stability Thermodynamics Machine Learning Proteins
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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 Azepines Protein Binding Cell Cycle Proteins Bromodomain Containing Proteins Nuclear Proteins Molecular Dynamics Simulation Binding Sites Transcription Factors Triazoles Thermodynamics
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