AIMC Topic: Proteome

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DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method.

International journal of molecular sciences May 24, 2021
It is essential for future research to develop a new, reliable prediction method of DNA binding sites because DNA binding sites on DNA-binding proteins provide critical clues about protein function and drug discovery. However, the current prediction ...
Humans Software DNA DNA-Binding Proteins Protein Conformation Binding Sites Animals Deep Learning Computational Biology Proteome
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pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning.

Journal of proteome research Apr 6, 2021
In cross-linking mass spectrometry, the identification of cross-linked peptide pairs heavily relies on the ability of a database search engine to measure the similarities between experimental and theoretical MS/MS spectra. However, the lack of accura...
Proteome Tandem Mass Spectrometry Algorithms Peptides Deep Learning Neural Networks, Computer
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Proteome analysis using machine learning approaches and its applications to diseases.

Advances in protein chemistry and structural biology Mar 24, 2021
With the tremendous developments in the fields of biological and medical technologies, huge amounts of data are generated in the form of genomic data, images in medical databases or as data on protein sequences, and so on. Analyzing this data through...
Proteome Databases, Protein Humans Deep Learning Proteomics
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Predicting Proteolysis in Complex Proteomes Using Deep Learning.

International journal of molecular sciences Mar 17, 2021
Both protease- and reactive oxygen species (ROS)-mediated proteolysis are thought to be key effectors of tissue remodeling. We have previously shown that comparison of amino acid composition can predict the differential susceptibilities of proteins t...
Reactive Oxygen Species Amino Acids Ultraviolet Rays Proteolysis Peptide Hydrolases Extracellular Matrix Proteins Software Reproducibility of Results Deep Learning Proteome Humans Neural Networks, Computer
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Deep learning the collisional cross sections of the peptide universe from a million experimental values.

Nature communications Feb 19, 2021
The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million dat...
Saccharomyces cerevisiae Drosophila melanogaster Caenorhabditis elegans Proteomics Proteome Escherichia coli Workflow Amino Acid Sequence Tandem Mass Spectrometry Ions Neural Networks, Computer HeLa Cells Animals Humans Peptides Deep Learning
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Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response.

Frontiers in immunology Feb 18, 2021
Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, div...
Proteome Viral Proteins Machine Learning Humans Epitopes, T-Lymphocyte HIV CD8-Positive T-Lymphocytes Antigens, Viral Genetic Variation HLA Antigens Peptides Host-Pathogen Interactions HIV Infections Genome, Viral
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Systematic auditing is essential to debiasing machine learning in biology.

Communications biology Feb 10, 2021
Biases in data used to train machine learning (ML) models can inflate their prediction performance and confound our understanding of how and what they learn. Although biases are common in biological data, systematic auditing of ML models to identify ...
Pharmaceutical Preparations Data Mining Histocompatibility Antigens Protein Interaction Maps Protein Binding Proteomics Proteome Proteins Databases, Protein Bias Humans Machine Learning Reproducibility of Results Animals
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Computational identification of ubiquitination sites in Arabidopsis thaliana using convolutional neural networks.

Plant molecular biology Feb 1, 2021
We developed two CNNs for predicting ubiquitination sites in Arabidopsis thaliana, demonstrated their competitive performance, analyzed amino acid physicochemical properties and the CNN structures, and predicted ubiquitination sites in Arabidopsis. A...
Humans Neural Networks, Computer Software Animals Protein Processing, Post-Translational Amino Acids Yeasts Ubiquitination Mice Computational Biology Proteome Arabidopsis
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Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2 leading to universal blueprints for vaccine designs.

Scientific reports Dec 23, 2020
The global population is at present suffering from a pandemic of Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The goal of this study was to use artificial intellige...
Proteome Machine Learning Mutation Humans Software COVID-19 Vaccines COVID-19 HLA Antigens Alleles Immunogenicity, Vaccine Pandemics Spike Glycoprotein, Coronavirus Algorithms Drug Evaluation, Preclinical Proteomics Amino Acid Sequence SARS-CoV-2 Haplotypes Epitopes, T-Lymphocyte
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PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids.

Genes Nov 28, 2020
Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant...
Protein Processing, Post-Translational Databases, Protein Lysine Computational Biology Proteome Support Vector Machine
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