AI Medical Compendium Topic:
Protein Binding

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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...
Epitopes, T-Lymphocyte Humans Peptides Software Deep Learning T-Lymphocytes Receptors, Antigen, T-Cell Protein Binding Signal Transduction Databases, Protein Ligands Antigens Binding Sites Protein Interaction Domains and Motifs
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A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes.

Nature communications Aug 21, 2020
Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identif...
Cell Survival Ligands HeLa Cells Saccharomyces cerevisiae Proteomics Proteome Mass Spectrometry Proteolysis Binding Sites Phosphotransferases Botrytis Humans Machine Learning Drug Delivery Systems Drug Discovery Protein Binding Computational Biology
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Comprehensive Prediction of Molecular Recognition in a Combinatorial Chemical Space Using Machine Learning.

ACS combinatorial science Aug 17, 2020
In combinatorial chemical approaches, optimizing the composition and arrangement of building blocks toward a particular function has been done using a number of methods, including high throughput molecular screening, molecular evolution, and computat...
Machine Learning Peptides Protein Binding Peptide Library Amino Acid Sequence Ligands High-Throughput Screening Assays Combinatorial Chemistry Techniques Structure-Activity Relationship Models, Molecular Molecular Structure
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Predictive modeling of estrogen receptor agonism, antagonism, and binding activities using machine- and deep-learning approaches.

Laboratory investigation; a journal of technical methods and pathology Aug 10, 2020
As defined by the World Health Organization, an endocrine disruptor is an exogenous substance or mixture that alters function(s) of the endocrine system and consequently causes adverse health effects in an intact organism, its progeny, or (sub)popula...
Endocrine Disruptors Receptors, Estrogen Computational Biology Humans Models, Statistical Machine Learning Databases, Chemical Algorithms Animals Deep Learning Protein Binding Mice
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Enhancing the interpretability of transcription factor binding site prediction using attention mechanism.

Scientific reports Aug 7, 2020
Transcription factors (TFs) regulate the gene expression of their target genes by binding to the regulatory sequences of target genes (e.g., promoters and enhancers). To fully understand gene regulatory mechanisms, it is crucial to decipher the relat...
Neural Networks, Computer Forecasting Transcription Factors Gene Expression Regulation Base Sequence Binding Sites Deep Learning Protein Binding Computational Biology Models, Theoretical
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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...
Protein Binding Databases, Protein HLA Antigens Ligands Humans Machine Learning Epitopes, T-Lymphocyte Histocompatibility Antigens Class II High-Throughput Screening Assays Protein Array Analysis Antigen Presentation Binding Sites CD4 Antigens Protein Interaction Domains and Motifs
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Moonlighting Proteins in the Fuzzy Logic of Cellular Metabolism.

Molecules (Basel, Switzerland) Jul 29, 2020
The numerous interconnected biochemical pathways that make up the metabolism of a living cell comprise a fuzzy logic system because of its high level of complexity and our inability to fully understand, predict, and model the many activities, how the...
Humans Animals Protein Binding Energy Metabolism Fuzzy Logic Proteins Metabolic Networks and Pathways Models, Biological
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Identification of ligand-binding residues using protein sequence profile alignment and query-specific support vector machine model.

Analytical biochemistry Jul 2, 2020
Information embedded in ligand-binding residues (LBRs) of proteins is important for understanding protein functions. How to accurately identify the potential ligand-binding residues is still a challenging problem, especially only protein sequence is ...
Binding Sites Proteins Databases, Protein Amino Acid Sequence Ligands Protein Binding Support Vector Machine
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Predicting protein subcellular location with network embedding and enrichment features.

Biochimica et biophysica acta. Proteins and proteomics Jun 25, 2020
The subcellular location of a protein is highly related to its function. Identifying the location of a given protein is an essential step for investigating its related problems. Traditional experimental methods can produce solid determination. Howeve...
Neural Networks, Computer Gene Ontology Protein Interaction Mapping Intracellular Space Computational Biology Algorithms Decision Trees Protein Interaction Maps Proteins Protein Binding Protein Transport
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IConMHC: a deep learning convolutional neural network model to predict peptide and MHC-I binding affinity.

Immunogenetics Jun 24, 2020
Tumor-specific neoantigens are mutated self-peptides presented by tumor cell major histocompatibility complex (MHC) molecules and are necessary to elicit host's anti-cancer cytotoxic T cell responses. It could be specifically recognized by neoantigen...
Humans Neural Networks, Computer Computer Simulation Reproducibility of Results Amino Acid Sequence Antigens, Neoplasm Databases, Protein Alleles Peptides Histocompatibility Antigens Class I Deep Learning Protein Binding
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