Molecular Dynamics Simulation

Discovery of hematopoietic progenitor kinase 1 inhibitors using machine learning-based screening and free energy perturbation.

Journal of biomolecular structure & dynamics Jan 10, 2024

Hematopoietic progenitor kinase 1 (HPK1) is a key negative regulator of T-cell receptor (TCR) signaling and a promising target for cancer immunotherapy. The development of novel HPK1 inhibitors is challenging yet promising. In this study, we used a c...

Humans Protein Serine-Threonine Kinases Structure-Activity Relationship Molecular Dynamics Simulation Protein Kinase Inhibitors Thermodynamics Machine Learning T-Lymphocytes Molecular Docking Simulation Drug Discovery Protein Binding Signal Transduction

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Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints.

Molecular diversity Jan 10, 2024

Cyclooxygenase-2 (COX-2) inhibitors are nonsteroidal anti-inflammatory drugs that treat inflammation, pain and fever. This study determined the interaction mechanisms of COX-2 inhibitors and the molecular properties needed to design new drug candidat...

Molecular Docking Simulation Computational Biology Phenols Artificial Intelligence Machine Learning Cyclooxygenase 2 Inhibitors Cyclooxygenase 2 Molecular Dynamics Simulation Ligands Hydrophobic and Hydrophilic Interactions

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Classification of MLH1 Missense VUS Using Protein Structure-Based Deep Learning-Ramachandran Plot-Molecular Dynamics Simulations Method.

International journal of molecular sciences Jan 10, 2024

Pathogenic variation in DNA mismatch repair (MMR) gene is associated with Lynch syndrome (LS), an autosomal dominant hereditary cancer. Of the 3798 germline variants collected in the ClinVar database, 38.7% (1469) were missense variants, of which 8...

MutL Protein Homolog 1 Humans Databases, Factual Deep Learning DNA Mismatch Repair Molecular Dynamics Simulation Colorectal Neoplasms, Hereditary Nonpolyposis

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Analyzing Molecular Dynamics Trajectories Thermodynamically through Artificial Intelligence.

Journal of chemical theory and computation Jan 9, 2024

Molecular dynamics simulations produce trajectories that correspond to vast amounts of structure when exploring biochemical processes. Extracting valuable information, e.g., important intermediate states and collective variables (CVs) that describe t...

Algorithms Molecular Dynamics Simulation Entropy Artificial Intelligence

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Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase.

Scientific reports Jan 2, 2024

Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout. This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used molecular docking to obtain three systems and then conducted 200 ns molecular dynam...

Humans Peptides Molecular Docking Simulation Molecular Dynamics Simulation Enzyme Inhibitors Xanthine Oxidase Deep Learning Structure-Activity Relationship Hyperuricemia

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Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.

Biophysical journal Dec 30, 2023

Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions tha...

Drosophila Proteins Machine Learning Static Electricity Animals Tubulin Protein Binding Protein Multimerization Ions Molecular Dynamics Simulation Kinesins Solvents Microtubules

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A computational tumor growth model experience based on molecular dynamics point of view using deep cellular automata.

Artificial intelligence in medicine Dec 27, 2023

Cancer, as identified by the World Health Organization, stands as the second leading cause of death globally. Its intricate nature makes it challenging to study solely based on biological knowledge, often leading to expensive research endeavors. Whil...

Models, Biological Molecular Dynamics Simulation Neoplasms Deep Learning Cellular Automata Humans Artificial Intelligence Tumor Microenvironment

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Investigating the bispecific lead compounds against methicillin-resistant SarA and CrtM using machine learning and molecular dynamics approach.

Journal of biomolecular structure & dynamics Dec 26, 2023

Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious pathogen that has emerged as a serious global health concern over the past few decades. Staphylococcal accessory regulator A (SarA) and 4,4'-diapophytoene synthase (CrtM) play a crucia...

Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Hydrogen Bonding Protein Binding Anti-Bacterial Agents Methicillin-Resistant Staphylococcus aureus Bacterial Proteins Molecular Docking Simulation Machine Learning Biofilms

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Deep learning-based design and screening of benzimidazole-pyrazine derivatives as adenosine A receptor antagonists.

Journal of biomolecular structure & dynamics Dec 22, 2023

The Adenosine A receptor (AAR) is considered a novel potential target for the immunotherapy of cancer, and AAR antagonists have an inhibitory effect on tumor growth, proliferation, and metastasis. In our previous studies, we identified a class of ben...

Humans Molecular Docking Simulation Drug Design Deep Learning Protein Binding Pyrazines Benzimidazoles Structure-Activity Relationship Adenosine A2 Receptor Antagonists Molecular Structure Receptor, Adenosine A2B Molecular Dynamics Simulation

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Identification of active compounds as novel dipeptidyl peptidase-4 inhibitors through machine learning and structure-based molecular docking simulations.

Journal of biomolecular structure & dynamics Dec 15, 2023

The enzyme dipeptidyl peptidase 4 (DPP4) is a potential therapeutic target for type 2 diabetes (T2DM). Many synthetic anti-DPP4 medications are available to treat T2DM. The need for secure and efficient medicines has been unmet due to the adverse sid...

Binding Sites Sitagliptin Phosphate Dipeptidyl-Peptidase IV Inhibitors Structure-Activity Relationship Molecular Dynamics Simulation Dipeptidyl Peptidase 4 Humans Neural Networks, Computer Machine Learning Molecular Docking Simulation Diabetes Mellitus, Type 2 Protein Binding

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

Discovery of hematopoietic progenitor kinase 1 inhibitors using machine learning-based screening and free energy perturbation.

Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints.

Classification of MLH1 Missense VUS Using Protein Structure-Based Deep Learning-Ramachandran Plot-Molecular Dynamics Simulations Method.

Analyzing Molecular Dynamics Trajectories Thermodynamically through Artificial Intelligence.

Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase.

Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.

A computational tumor growth model experience based on molecular dynamics point of view using deep cellular automata.

Investigating the bispecific lead compounds against methicillin-resistant SarA and CrtM using machine learning and molecular dynamics approach.

Deep learning-based design and screening of benzimidazole-pyrazine derivatives as adenosine A receptor antagonists.

Identification of active compounds as novel dipeptidyl peptidase-4 inhibitors through machine learning and structure-based molecular docking simulations.

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