AIMC Topic: Protein Processing, Post-Translational

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Identify and analysis crotonylation sites in histone by using support vector machines.

Artificial intelligence in medicine Mar 7, 2017
OBJECTIVE: Lysine crotonylation (Kcr) is a newly discovered histone posttranslational modification, which is specifically enriched at active gene promoters and potential enhancers in mammalian cell genomes. Although lysine crotonylation sites can be ...
Reproducibility of Results Animals Mice Humans Databases, Protein Amino Acid Sequence Lysine Histones Computational Biology Support Vector Machine Protein Processing, Post-Translational
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Systematic analysis of non-structural protein features for the prediction of PTM function potential by artificial neural networks.

PloS one Feb 22, 2017
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our k...
Protein Processing, Post-Translational Databases, Protein Proteome Mass Spectrometry Neural Networks, Computer Algorithms
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A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions.

BMC bioinformatics Aug 17, 2016
BACKGROUND: One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR ca...
Protein Processing, Post-Translational Proteins Protein Interaction Domains and Motifs Machine Learning
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Positive-Unlabeled Learning for Pupylation Sites Prediction.

BioMed research international Aug 7, 2016
Pupylation plays a key role in regulating various protein functions as a crucial posttranslational modification of prokaryotes. In order to understand the molecular mechanism of pupylation, it is important to identify pupylation substrates and sites ...
Protein Processing, Post-Translational Proteins Databases, Protein Machine Learning Lysine Binding Sites Algorithms Ubiquitination Support Vector Machine
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A machine-learning approach for predicting palmitoylation sites from integrated sequence-based features.

Journal of bioinformatics and computational biology Jun 14, 2016
Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, orga...
Algorithms Colorectal Neoplasms Computational Biology Support Vector Machine Humans Machine Learning Amino Acids Lipoylation Protein Processing, Post-Translational Proteins Databases, Protein
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Predicting pupylation sites in prokaryotic proteins using semi-supervised self-training support vector machine algorithm.

Analytical biochemistry May 16, 2016
As one important post-translational modification of prokaryotic proteins, pupylation plays a key role in regulating various biological processes. The accurate identification of pupylation sites is crucial for understanding the underlying mechanisms o...
Protein Processing, Post-Translational Bacterial Proteins Rhodococcus Algorithms Support Vector Machine Corynebacterium glutamicum
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A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.

PLoS computational biology Apr 7, 2016
O-linked glycosylation is an important post-translational modification of mucin-type protein, changes to which are important biomarkers of cancer. For this study of the enzymes of O-glycosylation, we developed a shorthand notation for representing Ga...
Genetic Engineering Polysaccharides Knowledge Bases Mucins Terminology as Topic Animals Gene Knockout Techniques Cricetulus Computational Biology Glycosyltransferases Metabolic Networks and Pathways Humans Glycosylation Models, Biological Computer Simulation Protein Processing, Post-Translational CHO Cells
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Predicting lysine phosphoglycerylation with fuzzy SVM by incorporating k-spaced amino acid pairs into Chou׳s general PseAAC.

Journal of theoretical biology Feb 22, 2016
As a new type of post-translational modification, lysine phosphoglycerylation plays a key role in regulating glycolytic process and metabolism in cells. Due to the traditional experimental methods are time-consuming and labor-intensive, it is importa...
Algorithms Reproducibility of Results Software Lysine Binding Sites Protein Processing, Post-Translational Diphosphoglyceric Acids Amino Acids Computational Biology Amino Acid Sequence Support Vector Machine Fuzzy Logic
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Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.

BMC bioinformatics Jan 11, 2016
BACKGROUND: Understanding the mechanisms by which transcription factors (TF) are recruited to their physiological target sites is crucial for understanding gene regulation. DNA sequence intrinsic features such as predicted binding affinity are often ...
Cell Lineage Humans Algorithms Chromatin Genome, Human Nucleosomes Machine Learning Transcription Factors Protein Processing, Post-Translational Chromatin Immunoprecipitation Histones DNA Binding Sites Gene Expression Regulation
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Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation.

BioMed research international Oct 27, 2015
Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much at...
Proteins Rats Gene Ontology Humans Phosphorylation Animals Protein Processing, Post-Translational Amino Acid Motifs Dogs Mice Evolution, Molecular Acylation
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