AIMC Topic: Protein Interaction Domains and Motifs

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Prediction of Specific TCR-Peptide Binding From Large Dictionaries of TCR-Peptide Pairs.

Frontiers in immunology Aug 25, 2020
Current sequencing methods allow for detailed samples of T cell receptors (TCR) repertoires. To determine from a repertoire whether its host had been exposed to a target, computational tools that predict TCR-epitope binding are required. Currents too...
Protein Binding Signal Transduction Databases, Protein Ligands Antigens Binding Sites Protein Interaction Domains and Motifs Epitopes, T-Lymphocyte Peptides Deep Learning Receptors, Antigen, T-Cell Humans Software T-Lymphocytes
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Unbiased Characterization of Peptide-HLA Class II Interactions Based on Large-Scale Peptide Microarrays; Assessment of the Impact on HLA Class II Ligand and Epitope Prediction.

Frontiers in immunology Aug 5, 2020
Human Leukocyte Antigen class II (HLA-II) molecules present peptides to T lymphocytes and play an important role in adaptive immune responses. Characterizing the binding specificity of single HLA-II molecules has profound impacts for understanding ce...
Humans Machine Learning Histocompatibility Antigens Class II Ligands High-Throughput Screening Assays Antigen Presentation Epitopes, T-Lymphocyte Protein Array Analysis CD4 Antigens Protein Binding Binding Sites Databases, Protein Protein Interaction Domains and Motifs HLA Antigens
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Rosetta custom score functions accurately predict ΔΔG of mutations at protein-protein interfaces using machine learning.

Chemical communications (Cambridge, England) May 22, 2020
Protein-protein interfaces play essential roles in a variety of biological processes and many therapeutic molecules are targeted at these interfaces. However, accurate predictions of the effects of interfacial mutations to identify "hotspots" have re...
Machine Learning Proteins Mutation Protein Interaction Domains and Motifs
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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...
Protein Interaction Mapping Protein Multimerization Protein Interaction Domains and Motifs Structural Homology, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Humans Software Research Design Peptides Molecular Docking Simulation Deep Learning Ligands Binding Sites Thermodynamics Computer Graphics Protein Binding Proteins Benchmarking Amino Acid Sequence
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Sequence-Based Prediction of Fuzzy Protein Interactions.

Journal of molecular biology Feb 27, 2020
It is becoming increasingly recognised that disordered proteins may be fuzzy, in that they can exhibit a wide variety of binding modes. In addition to the well-known process of folding upon binding (disorder-to-order transition), many examples are em...
Amino Acid Sequence Intrinsically Disordered Proteins Protein Conformation Protein Folding Sequence Analysis, Protein Fuzzy Logic Databases, Protein Models, Molecular Protein Domains Protein Interaction Domains and Motifs Sequence Homology Humans Algorithms Protein Binding
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Computational Identification and Analysis of Ubiquinone-Binding Proteins.

Cells Feb 24, 2020
Ubiquinone is an important cofactor that plays vital and diverse roles in many biological processes. Ubiquinone-binding proteins (UBPs) are receptor proteins that dock with ubiquinones. Analyzing and identifying UBPs via a computational approach will...
Protein Binding Computational Biology Membrane Proteins Carrier Proteins Amino Acid Sequence Humans Protein Interaction Domains and Motifs Machine Learning Position-Specific Scoring Matrices Ubiquinone Gene Ontology Binding Sites Sequence Analysis, Protein
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Discovery of Small-Molecule Activators for Glucose-6-Phosphate Dehydrogenase (G6PD) Using Machine Learning Approaches.

International journal of molecular sciences Feb 23, 2020
Glucose-6-Phosphate Dehydrogenase (G6PD) is a ubiquitous cytoplasmic enzyme converting glucose-6-phosphate into 6-phosphogluconate in the pentose phosphate pathway (PPP). The G6PD deficiency renders the inability to regenerate glutathione due to lack...
Protein Interaction Domains and Motifs Glucosephosphate Dehydrogenase Molecular Docking Simulation NADP Drug Discovery Pentose Phosphate Pathway Oxidative Stress Glucosephosphate Dehydrogenase Deficiency Oxidation-Reduction Drug Evaluation, Preclinical Humans Catalytic Domain Machine Learning Glutathione Animals X-Ray Diffraction
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Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs.

Scientific reports Feb 11, 2020
Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational...
Animals Protein Interaction Maps Gene Regulatory Networks Proteome Insect Proteins Genome, Insect Ants Molecular Sequence Annotation Gene Ontology Protein Interaction Domains and Motifs
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Analysis of the Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach.

International journal of molecular sciences Jun 18, 2019
Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk facto...
Protein Interaction Domains and Motifs Humans Neural Networks, Computer Machine Learning Molecular Docking Simulation Mutation Molecular Dynamics Simulation Protein Binding Tumor Suppressor Protein p53 Polymorphism, Single Nucleotide Protein Conformation Computational Biology Estrogen Receptor alpha Structure-Activity Relationship
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife Jun 21, 2018
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Serotonin 5-HT2 Receptor Antagonists Protein Stability Protein Conformation, alpha-Helical Protein Engineering Models, Molecular Protein Conformation, beta-Strand Receptor, Serotonin, 5-HT2C Thermodynamics Gene Expression Point Mutation Crystallography, X-Ray Sequence Alignment Kinetics Serotonin 5-HT2 Receptor Agonists Binding Sites Sequence Homology, Amino Acid Amino Acid Sequence Humans Protein Interaction Domains and Motifs Machine Learning Animals Protein Binding
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