Protein Binding

Evaluating NetMHCpan performance on non-European HLA alleles not present in training data.

Frontiers in immunology Jan 16, 2024

Bias in neural network model training datasets has been observed to decrease prediction accuracy for groups underrepresented in training data. Thus, investigating the composition of training datasets used in machine learning models with healthcare ap...

Alleles Histocompatibility Antigens Class I Genes, MHC Class I Humans Peptides Protein Binding

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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...

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

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T6496 targeting EGFR mediated by T790M or C797S mutant: machine learning, virtual screening and bioactivity evaluation study.

Journal of biomolecular structure & dynamics Jan 4, 2024

Acquired resistance to EGFR is a major impediment in lung cancer treatment, highlighting the urgent need to discover novel compounds to overcome EGFR drug resistance. In this study, we utilized in silico methods and bioactivity evaluation for drug di...

Antineoplastic Agents Humans Cell Line, Tumor Protein Binding Machine Learning Mutation Drug Resistance, Neoplasm Molecular Docking Simulation Drug Discovery ErbB Receptors Cell Proliferation Protein Kinase Inhibitors Apoptosis Drug Screening Assays, Antitumor

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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...

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

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Harnessing deep learning for enhanced ligand docking.

Trends in pharmacological sciences Dec 30, 2023

Ligand docking (LD), a technology for predicting protein-ligand (PL)-binding conformations and strengths, plays key roles in virtual screening (VS). However, the accuracy and speed of current LD methodologies remain suboptimal. Here, we discuss how d...

Protein Binding Proteins Humans Ligands Molecular Docking Simulation Protein Conformation 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...

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

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

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Evaluation of DNA-protein complex structures using the deep learning method.

Physical chemistry chemical physics : PCCP Dec 21, 2023

Biological processes such as transcription, repair, and regulation require interactions between DNA and proteins. To unravel their functions, it is imperative to determine the high-resolution structures of DNA-protein complexes. However, experimental...

Deep Learning Protein Binding Proteins DNA Neural Networks, Computer Research 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...

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

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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...

High-Throughput Screening Assays Quantitative Structure-Activity Relationship Protein Kinase Inhibitors Protein Binding Proto-Oncogene Proteins c-akt Molecular Dynamics Simulation Allosteric Regulation Humans Machine Learning Molecular Docking Simulation Drug Discovery

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AI Medical Compendium Topic

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

Evaluating NetMHCpan performance on non-European HLA alleles not present in training data.

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

T6496 targeting EGFR mediated by T790M or C797S mutant: machine learning, virtual screening and bioactivity evaluation study.

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

Harnessing deep learning for enhanced ligand docking.

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.

Evaluation of DNA-protein complex structures using the deep learning method.

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

Integrating machine learning and high throughput screening for the discovery of allosteric AKT1 inhibitors.

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