AIMC Topic: Amino Acid Motifs

Clear Filters Showing 21 to 30 of 37 articles

ProtDet-CCH: Protein Remote Homology Detection by Combining Long Short-Term Memory and Ranking Methods.

IEEE/ACM transactions on computational biology and bioinformatics Jan 5, 2018
As one of the most challenging tasks in sequence analysis, protein remote homology detection has been extensively studied. Methods based on discriminative models and ranking approaches have achieved the state-of-the-art performance, and these two kin...
Humans Neural Networks, Computer Software Algorithms Proteins Databases, Protein Sequence Homology, Amino Acid Amino Acid Motifs Sequence Analysis, Protein Databases, Factual Reproducibility of Results Computational Biology Support Vector Machine
View on PubMed DOI

ApoplastP: prediction of effectors and plant proteins in the apoplast using machine learning.

The New phytologist Dec 15, 2017
The plant apoplast is integral to intercellular signalling, transport and plant-pathogen interactions. Plant pathogens deliver effectors both into the apoplast and inside host cells, but no computational method currently exists to discriminate betwee...
Conserved Sequence Amino Acid Motifs Protein Sorting Signals Oomycetes Machine Learning Plant Proteins Fungal Proteins Cysteine Proteomics Amino Acid Sequence
View on PubMed DOI

Sequence-Based Prediction of Cysteine Reactivity Using Machine Learning.

Biochemistry Oct 26, 2017
As one of the most intrinsically reactive amino acids, cysteine carries a variety of important biochemical functions, including catalysis and redox regulation. Discovery and characterization of cysteines with heightened reactivity will help annotate ...
Cysteine Sequence Alignment Amino Acid Motifs Proteomics Chromatography, Liquid Tandem Mass Spectrometry Humans Escherichia coli Proteins Machine Learning Decision Support Techniques Recombinant Proteins
View on PubMed DOI

Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues.

Scientific reports Dec 21, 2016
The Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a com...
Gene Expression Profiling Real-Time Polymerase Chain Reaction Liver Neoplasms Carcinoma, Hepatocellular Humans Machine Learning Algorithms Phylogeny Cluster Analysis Protein Domains Amino Acid Motifs GTPase-Activating Proteins Dishevelled Proteins Computational Biology RNA, Messenger Gene Expression Regulation, Neoplastic Signal Transduction
View on PubMed DOI

A Graph Approach to Mining Biological Patterns in the Binding Interfaces.

Journal of computational biology : a journal of computational molecular cell biology Nov 28, 2016
Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, ...
Proteins Data Mining RNA Protein Conformation Binding Sites Computer Graphics Amino Acid Motifs Protein Interaction Domains and Motifs Protein Binding Computational Biology RNA-Binding Proteins Support Vector Machine Humans Animals Molecular Docking Simulation
View on PubMed DOI

Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus.

Traffic (Copenhagen, Denmark) Aug 22, 2016
The peroxisomal targeting signal type 1 (PTS1) is a seemingly simple peptide sequence at the C-terminal end of most peroxisomal matrix proteins. PTS1 can be described as a tripeptide with the consensus motif [S/A/C] [K/R/H] L. However, this descripti...
Peroxisome-Targeting Signal 1 Receptor Databases, Genetic Saccharomyces cerevisiae Receptors, Cytoplasmic and Nuclear Peroxisomes Machine Learning Protein Sorting Signals Genome-Wide Association Study Genome, Fungal Saccharomyces cerevisiae Proteins Consensus Sequence Amino Acid Motifs
View on PubMed DOI

In Silico Prediction of Gamma-Aminobutyric Acid Type-A Receptors Using Novel Machine-Learning-Based SVM and GBDT Approaches.

BioMed research international Aug 8, 2016
Gamma-aminobutyric acid type-A receptors (GABAARs) belong to multisubunit membrane spanning ligand-gated ion channels (LGICs) which act as the principal mediators of rapid inhibitory synaptic transmission in the human brain. Therefore, the category p...
Amino Acids Ligands Amino Acid Motifs Receptors, GABA-A Decision Making Models, Statistical Decision Trees Databases, Protein Brain Humans Computer Simulation Reproducibility of Results Machine Learning Computational Biology Algorithms Support Vector Machine
View on PubMed DOI

UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.

BMC systems biology Jan 11, 2016
BACKGROUND: The conjugation of ubiquitin to a substrate protein (protein ubiquitylation), which involves a sequential process--E1 activation, E2 conjugation and E3 ligation, is crucial to the regulation of protein function and activity in eukaryotes....
Machine Learning Software Proteomics Proteome Mass Spectrometry Models, Molecular Protein Domains Amino Acid Sequence Amino Acid Motifs Sequence Analysis, Protein Datasets as Topic Lysine Ubiquitin Ubiquitination
View on PubMed DOI

A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs.

BMC bioinformatics Dec 9, 2015
Protein O-GlcNAcylation, involving the β-attachment of single N-acetylglucosamine (GlcNAc) to the hydroxyl group of serine or threonine residues, is an O-linked glycosylation catalyzed by O-GlcNAc transferase (OGT). Molecular level investigation of t...
Proteins Internet Substrate Specificity Amino Acid Motifs Glycosylation N-Acetylglucosaminyltransferases Support Vector Machine Mass Spectrometry Acetylglucosamine Machine Learning Algorithms Peptides User-Computer Interface
View on PubMed DOI

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...
Phosphorylation Dogs Gene Ontology Amino Acid Motifs Rats Protein Processing, Post-Translational Evolution, Molecular Proteins Acylation Humans Animals Mice
View on PubMed DOI
Popular Topics
Recent Journals