AIMC Topic: Peptide Library

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Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches.

International journal of molecular sciences Apr 25, 2023
Protein-protein interfaces play fundamental roles in the molecular mechanisms underlying pathophysiological pathways and are important targets for the design of compounds of therapeutic interest. However, the identification of binding sites on protei...
Peptides Protein Binding Peptide Library Membrane Proteins Binding Sites Artificial Intelligence
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DeepDetect: Deep Learning of Peptide Detectability Enhanced by Peptide Digestibility and Its Application to DIA Library Reduction.

Analytical chemistry Mar 12, 2023
In tandem mass spectrometry-based proteomics, proteins are digested into peptides by specific protease(s), but generally only a fraction of peptides can be detected. To characterize detectable proteotypic peptides, we have developed a series of metho...
Mice Peptide Library Proteome Escherichia coli Proteins Humans Animals Peptides Deep Learning Tandem Mass Spectrometry Saccharomyces cerevisiae Peptide Hydrolases
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Decoding CAR T cell phenotype using combinatorial signaling motif libraries and machine learning.

Science (New York, N.Y.) Dec 8, 2022
Chimeric antigen receptor (CAR) costimulatory domains derived from native immune receptors steer the phenotypic output of therapeutic T cells. We constructed a library of CARs containing ~2300 synthetic costimulatory domains, built from combinations ...
Humans Machine Learning Phenotype Signal Transduction Receptors, Chimeric Antigen Protein Domains Peptide Library T-Lymphocytes, Cytotoxic
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DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation.

Nature communications Nov 18, 2021
Phosphoproteomics integrating data-independent acquisition (DIA) enables deep phosphoproteome profiling with improved quantification reproducibility and accuracy compared to data-dependent acquisition (DDA)-based phosphoproteomics. DIA data mining he...
Algorithms Computer Simulation Reproducibility of Results Deep Learning Cell Line, Tumor Humans Phosphopeptides Chromatography, Liquid Phosphoproteins Tandem Mass Spectrometry Peptide Library Data Mining Computational Biology Proteomics Proteome
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Screening of a novel free fatty acid receptor 1 (FFAR1) agonist peptide by phage display and machine learning based-amino acid substitution.

Biochemical and biophysical research communications Mar 9, 2021
Free fatty acid receptor 1 (FFAR1 or GPR40) has attracted attention for the treatment of type 2 diabetes mellitus, and various small-molecule agonists have been developed. However, most FFAR1 agonists as well as endogenous ligands, such as linoleic a...
Glucose Drug Evaluation, Preclinical Amino Acid Sequence HEK293 Cells Peptide Library Cell Line Regression Analysis Receptors, G-Protein-Coupled Cloning, Molecular Amino Acid Substitution Transforming Growth Factor alpha Peptides Insulin Protein Binding Humans Machine Learning
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Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning.

Frontiers in immunology Feb 10, 2021
The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achie...
DNA, Recombinant HIV Envelope Protein gp160 Hepatitis C Antigens Peptide Library Genetic Vectors Peptide Fragments DNA Barcoding, Taxonomic HIV Antibodies Oligonucleotides Epitopes Polymerase Chain Reaction Humans AIDS Serodiagnosis Hepatitis C Base Sequence Hepatitis C Antibodies Amino Acid Sequence Machine Learning Antigen-Antibody Reactions Serologic Tests HIV Core Protein p24 Communicable Diseases High-Throughput Nucleotide Sequencing HIV Infections
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Evolutionary artificial intelligence based peptide discoveries for effective Covid-19 therapeutics.

Biochimica et biophysica acta. Molecular basis of disease Sep 24, 2020
An epidemic caused by COVID-19 in China turned into pandemic within a short duration affecting countries worldwide. Researchers and companies around the world are working on all the possible strategies to develop a curative or preventive strategy for...
Antibodies, Viral Molecular Dynamics Simulation COVID-19 Drug Treatment Virus Replication Viral Vaccines Peptides Antiviral Agents Peptide Library Humans Artificial Intelligence COVID-19 SARS-CoV-2
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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...
Protein Binding Peptide Library Structure-Activity Relationship Models, Molecular Ligands High-Throughput Screening Assays Machine Learning Combinatorial Chemistry Techniques Molecular Structure Peptides Amino Acid Sequence
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In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics.

Nature communications Jan 9, 2020
Data-independent acquisition (DIA) is an emerging technology for quantitative proteomic analysis of large cohorts of samples. However, sample-specific spectral libraries built by data-dependent acquisition (DDA) experiments are required prior to DIA ...
Computer Simulation Animals Peptides Deep Learning Mice Peptide Library Computational Biology Data Science Cell Line, Tumor Humans Proteomics HeLa Cells Proteome Serum Mass Spectrometry Databases, Protein
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Introducing of an integrated artificial neural network and Chou's pseudo amino acid composition approach for computational epitope-mapping of Crimean-Congo haemorrhagic fever virus antigens.

International immunopharmacology Nov 24, 2019
This study was aimed to introduce a novel algorithm for determining linear B- and T-cell epitopes from Crimean-Congo haemorrhagic fever virus (CCHFV) antigens. To this end, 387 approved B- and T-cell epitopes, as well as 331 non-epitope peptides from...
Datasets as Topic Peptide Library Viral Proteins Computational Biology Antigens, Viral Humans Support Vector Machine Protein Structure, Tertiary Epitope Mapping Neural Networks, Computer Amino Acid Sequence Histocompatibility Antigens Class II Hemorrhagic Fever Virus, Crimean-Congo Epitopes, T-Lymphocyte Epitopes, B-Lymphocyte Hemorrhagic Fever, Crimean Molecular Docking Simulation
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