AIMC Topic: Peptides

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Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets.

Biochimica et biophysica acta. General subjects Jan 16, 2020
Selecting peptides that bind strongly to the major histocompatibility complex (MHC) for inclusion in a vaccine has therapeutic potential for infections and tumors. Machine learning models trained on sequence data exist for peptide:MHC (p:MHC) binding...
Mice Alleles Histocompatibility Antigens Class I Amino Acid Sequence Protein Conformation Animals Peptides Protein Binding Machine Learning Algorithms
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Machine intelligence in peptide therapeutics: A next-generation tool for rapid disease screening.

Medicinal research reviews Jan 10, 2020
Discovery and development of biopeptides are time-consuming, laborious, and dependent on various factors. Data-driven computational methods, especially machine learning (ML) approach, can rapidly and efficiently predict the utility of therapeutic pep...
Algorithms Animals Peptides Humans Artificial Intelligence Mass Screening Databases, Protein Disease
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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 ...
Humans Computer Simulation Animals HeLa Cells Serum Data Science Cell Line, Tumor Peptides Proteome Mice Peptide Library Deep Learning Mass Spectrometry Computational Biology Databases, Protein Proteomics
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Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.

Nature methods Jan 6, 2020
In mammalian cells, much of signal transduction is mediated by weak protein-protein interactions between globular peptide-binding domains (PBDs) and unstructured peptidic motifs in partner proteins. The number and diversity of these PBDs (over 1,800 ...
Humans Machine Learning Reproducibility of Results Proteins Peptides Biophysical Phenomena Protein Binding src Homology Domains Signal Transduction
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MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks.

BMC genomics Dec 24, 2019
BACKGROUND: Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database sea...
Deep Learning Humans Proteins Neural Networks, Computer Tandem Mass Spectrometry Peptides HeLa Cells Sequence Analysis, Protein
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Antimicrobial peptide identification using multi-scale convolutional network.

BMC bioinformatics Dec 23, 2019
BACKGROUND: Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine learning methods have been commo...
Humans Neural Networks, Computer Peptides
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iQSP: A Sequence-Based Tool for the Prediction and Analysis of Quorum Sensing Peptides via Chou's 5-Steps Rule and Informative Physicochemical Properties.

International journal of molecular sciences Dec 20, 2019
Understanding of quorum-sensing peptides (QSPs) in their functional mechanism plays an essential role in finding new opportunities to combat bacterial infections by designing drugs. With the avalanche of the newly available peptide sequences in the p...
Bacteria Support Vector Machine Models, Molecular Machine Learning Amino Acid Sequence Peptides Bacterial Physiological Phenomena Drug Discovery Quorum Sensing
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An antifouling peptide-based biosensor for determination of Streptococcus pneumonia markers in human serum.

Biosensors & bioelectronics Dec 19, 2019
We report a peptide-based sensor that involves a multivalent interaction with L-ascorbate 6-phosphate lactonase (UlaG), a protein marker of Streptococcus pneumonia. By integrating the antifouling feature of the sensor, we significantly improved the s...
Gold Pneumococcal Infections Peptides Humans Streptococcus pneumoniae Aptamers, Nucleotide Biomarkers Biosensing Techniques
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Prediction of the Health Effects of Food Peptides and Elucidation of the Mode-of-action Using Multi-task Graph Convolutional Neural Network.

Molecular informatics Nov 28, 2019
Food proteins work not only as nutrients but also modulators for the physiological functions of the human body. The physiological functions of food proteins are basically regulated by peptides encrypted in food protein sequences (food peptides). In t...
Peptides Molecular Docking Simulation Blood Glucose Algorithms Humans Antineoplastic Agents Neoplasms Blood Pressure Neural Networks, Computer
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MiPepid: MicroPeptide identification tool using machine learning.

BMC bioinformatics Nov 8, 2019
BACKGROUND: Micropeptides are small proteins with length < = 100 amino acids. Short open reading frames that could produces micropeptides were traditionally ignored due to technical difficulties, as few small peptides had been experimentally confirme...
Databases, Protein Open Reading Frames Software Peptides Computational Biology Machine Learning
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