AIMC Topic: Molecular Dynamics Simulation

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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...
Deep Learning Humans DNA Mismatch Repair Databases, Factual Molecular Dynamics Simulation Colorectal Neoplasms, Hereditary Nonpolyposis MutL Protein Homolog 1
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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 Deep Learning Molecular Dynamics Simulation Structure-Activity Relationship Enzyme Inhibitors Hyperuricemia Xanthine Oxidase
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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...
Solvents Microtubules Drosophila Proteins Molecular Dynamics Simulation Ions Kinesins Machine Learning Animals Static Electricity Protein Binding Tubulin Protein Multimerization
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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...
Cellular Automata Tumor Microenvironment Models, Biological Humans Molecular Dynamics Simulation Neoplasms Artificial Intelligence Deep Learning
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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 Methicillin-Resistant Staphylococcus aureus Bacterial Proteins Molecular Docking Simulation Biofilms Machine Learning Anti-Bacterial Agents
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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...
Molecular Dynamics Simulation Benzimidazoles Adenosine A2 Receptor Antagonists Pyrazines Receptor, Adenosine A2B Humans Structure-Activity Relationship Deep Learning Molecular Docking Simulation Molecular Structure Protein Binding Drug Design
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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...
Dipeptidyl-Peptidase IV Inhibitors Binding Sites Sitagliptin Phosphate Molecular Docking Simulation Diabetes Mellitus, Type 2 Protein Binding Structure-Activity Relationship Molecular Dynamics Simulation Dipeptidyl Peptidase 4 Humans Neural Networks, Computer Machine Learning
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Interpreting forces as deep learning gradients improves quality of predicted protein structures.

Biophysical journal Dec 15, 2023
Protein structure predictions from deep learning models like AlphaFold2, despite their remarkable accuracy, are likely insufficient for direct use in downstream tasks like molecular docking. The functionality of such models could be improved with a c...
Molecular Dynamics Simulation Protein Conformation Deep Learning Proteins
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Integrating machine learning and high throughput screening for the discovery of allosteric AKT1 inhibitors.

Journal of biomolecular structure & dynamics Dec 14, 2023
Evidence from clinical and experimental investigations reveals the role of AKT in oral cancer, which has led to the development of therapeutic and pharmacological medications for inhibiting AKT protein. Despite prodigious effort, researchers are sear...
Humans Machine Learning Proto-Oncogene Proteins c-akt Molecular Dynamics Simulation High-Throughput Screening Assays Molecular Docking Simulation Drug Discovery Protein Binding Allosteric Regulation Quantitative Structure-Activity Relationship Protein Kinase Inhibitors
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