AIMC Topic: Protein Multimerization

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DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes.

International journal of molecular sciences Apr 28, 2024
The molecular weight (MW) of an enzyme is a critical parameter in enzyme-constrained models (ecModels). It is determined by two factors: the presence of subunits and the abundance of each subunit. Although the number of subunits (NS) can potentially ...
Protein Multimerization Protein Subunits Deep Learning Mice Computational Biology Databases, Protein Humans Animals
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Inactive-enriched machine-learning models exploiting patent data improve structure-based virtual screening for PDL1 dimerizers.

Journal of advanced research Jan 26, 2024
INTRODUCTION: Small-molecule Programmable Cell Death Protein 1/Programmable Death-Ligand 1 (PD1/PDL1) inhibition via PDL1 dimerization has the potential to lead to inexpensive drugs with better cancer patient outcomes and milder side effects. However...
Machine Learning Drug Design B7-H1 Antigen Programmed Cell Death 1 Receptor Protein Multimerization Humans Patents as Topic
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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...
Animals Protein Binding Molecular Dynamics Simulation Ions Machine Learning Solvents Tubulin Microtubules Protein Multimerization Drosophila Proteins Kinesins Static Electricity
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Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers.

Proteins Apr 10, 2023
Probing the structures of amyloid-β (Aβ) peptides in the early steps of aggregation is extremely difficult experimentally and computationally. Yet, this knowledge is extremely important as small oligomers are the most toxic species. Experiments and s...
Humans Machine Learning Thermodynamics Protein Structure, Secondary Protein Multimerization Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Amyloid beta-Peptides Peptide Fragments Molecular Dynamics Simulation Protein Aggregates
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Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells adhered to laminin.

PLoS computational biology Nov 29, 2021
Sickle cell disease, a genetic disorder affecting a sizeable global demographic, manifests in sickle red blood cells (sRBCs) with altered shape and biomechanics. sRBCs show heightened adhesive interactions with inflamed endothelium, triggering painfu...
Biophysical Phenomena Lab-On-A-Chip Devices Laminin Protein Multimerization Microfluidics Anemia, Sickle Cell High-Throughput Screening Assays Image Interpretation, Computer-Assisted Erythrocytes, Abnormal Erythrocyte Deformability Hemoglobin, Sickle Humans Neural Networks, Computer Diagnosis, Computer-Assisted Deep Learning In Vitro Techniques Computational Biology
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Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation.

Chembiochem : a European journal of chemical biology Nov 17, 2020
Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved h...
Protein Multimerization Epoxide Hydrolases Rhodococcus Limonene Protein Engineering Protein Folding Machine Learning Mutation Molecular Dynamics Simulation
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A Two-Layer SVM Ensemble-Classifier to Predict Interface Residue Pairs of Protein Trimers.

Molecules (Basel, Switzerland) Sep 23, 2020
Study of interface residue pairs is important for understanding the interactions between monomers inside a trimer protein-protein complex. We developed a two-layer support vector machine (SVM) ensemble-classifier that considers physicochemical and ge...
Protein Structure, Quaternary Support Vector Machine Proteins Protein Multimerization Computational Biology
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Energy-based graph convolutional networks for scoring protein docking models.

Proteins Mar 16, 2020
Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative for su...
Humans Software Research Design Peptides Molecular Docking Simulation Deep Learning Protein Binding Binding Sites Thermodynamics Protein Multimerization Computer Graphics Protein Conformation, beta-Strand Protein Interaction Mapping Proteins Protein Interaction Domains and Motifs Structural Homology, Protein Benchmarking Protein Conformation, alpha-Helical Amino Acid Sequence Ligands
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers.

Progress in molecular biology and translational science Dec 6, 2019
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfam...
Humans Neural Networks, Computer Protein Binding Allosteric Site Computational Biology Machine Learning Support Vector Machine Software Receptors, G-Protein-Coupled Mutation Algorithms Molecular Dynamics Simulation Animals Crystallography, X-Ray Ligands Protein Interaction Mapping Fluorescence Resonance Energy Transfer Protein Structure, Secondary Protein Multimerization
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modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly.

The Journal of biological chemistry Sep 18, 2017
To understand the mechanism for assembly of Lys-linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys...
Point Mutation Ubiquitin-Conjugating Enzymes Ubiquitin Biocatalysis Ubiquitination Protein Conformation Protein Multimerization Cysteine Isoenzymes Computational Biology Humans Amino Acid Substitution Ubiquitin-Protein Ligases Models, Molecular Animals Molecular Docking Simulation Recombinant Fusion Proteins Iodine Radioisotopes Cattle Binding Sites Expert Systems Mutagenesis, Site-Directed
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