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Amino Acid Motifs

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

Journal of computational biology : a journal of computational molecular cell biology Jan 1, 2017
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, ...
Humans Animals RNA-Binding Proteins Support Vector Machine Proteins Molecular Docking Simulation Protein Binding Computational Biology Protein Interaction Domains and Motifs Binding Sites Computer Graphics Amino Acid Motifs Data Mining RNA Protein Conformation
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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...
Computational Biology RNA, Messenger Gene Expression Regulation, Neoplastic Real-Time Polymerase Chain Reaction Humans Liver Neoplasms Machine Learning Carcinoma, Hepatocellular Amino Acid Motifs Algorithms Phylogeny Signal Transduction GTPase-Activating Proteins Gene Expression Profiling Dishevelled Proteins Cluster Analysis Protein Domains
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Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus.

Traffic (Copenhagen, Denmark) Oct 1, 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 Protein Sorting Signals Genome, Fungal Consensus Sequence Databases, Genetic Saccharomyces cerevisiae Receptors, Cytoplasmic and Nuclear Peroxisomes Saccharomyces cerevisiae Proteins Amino Acid Motifs Machine Learning Genome-Wide Association Study
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MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs.

Bioinformatics (Oxford, England) Jan 15, 2016
UNLABELLED: S-sulfenylation (S-sulphenylation, or sulfenic acid), the covalent attachment of S-hydroxyl (-SOH) to cysteine thiol, plays a significant role in redox regulation of protein functions. Although sulfenic acid is transient and labile, most ...
Protein Processing, Post-Translational Proteins Amino Acids Humans Sulfur Acids Software Cysteine Support Vector Machine Amino Acid Motifs Sequence Analysis, Protein
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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....
Sequence Analysis, Protein Ubiquitin Ubiquitination Amino Acid Motifs Mass Spectrometry Models, Molecular Protein Domains Amino Acid Sequence Datasets as Topic Lysine Software Machine Learning Proteomics Proteome
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In Silico Prediction of Gamma-Aminobutyric Acid Type-A Receptors Using Novel Machine-Learning-Based SVM and GBDT Approaches.

BioMed research international Jan 1, 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...
Decision Making Models, Statistical Decision Trees Databases, Protein Amino Acids Ligands Amino Acid Motifs Humans Reproducibility of Results Receptors, GABA-A Machine Learning Algorithms Brain Computational Biology Computer Simulation Support Vector Machine
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Computer-Aided Virtual Screening and Designing of Cell-Penetrating Peptides.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2015
Cell-penetrating peptides (CPPs) have proven their potential as versatile drug delivery vehicles. Last decade has witnessed an unprecedented growth in CPP-based research, demonstrating the potential of CPPs as therapeutic candidates. In the past, man...
Drug Carriers Proteins Amino Acid Sequence Cell-Penetrating Peptides Molecular Sequence Data Animals Humans Amino Acid Motifs Machine Learning Computer-Aided Design Computer Simulation Support Vector Machine
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