AIMC Topic: Amino Acid Sequence

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Enhancing the Prediction of Transmembrane β-Barrel Segments with Chain Learning and Feature Sparse Representation.

IEEE/ACM transactions on computational biology and bioinformatics Feb 11, 2016
Transmembrane β-barrels (TMBs) are one important class of membrane proteins that play crucial functions in the cell. Membrane proteins are difficult wet-lab targets of structural biology, which call for accurate computational prediction approaches. H...
Machine Learning Algorithms Computer Simulation Pattern Recognition, Automated Protein Structure, Secondary Molecular Sequence Data Sequence Analysis, Protein Membrane Proteins Databases, Protein Models, Chemical Amino Acid Sequence
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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 Machine Learning Protein Domains Software Amino Acid Sequence Proteome Proteomics Datasets as Topic Mass Spectrometry Lysine Models, Molecular
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NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction.

Bioinformatics (Oxford, England) Dec 9, 2015
UNLABELLED: The nucleotide binding site leucine-rich repeats (NBSLRRs) belong to one of the largest known families of disease resistance genes that encode resistance proteins (R-protein) against the pathogens of plants. Various defence mechanisms hav...
Support Vector Machine Solanum lycopersicum Amino Acid Sequence Nucleotides Arabidopsis Plant Diseases Plant Proteins Conserved Sequence
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Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics.

PloS one Nov 10, 2015
We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (Gene...
Amino Acid Sequence Genomics Intrinsically Disordered Proteins Computational Biology Proteins Protein Structure, Secondary Proteomics Databases, Protein Nuclear Pore Complex Proteins Natural Language Processing Support Vector Machine
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DisPredict: A Predictor of Disordered Protein Using Optimized RBF Kernel.

PloS one Oct 30, 2015
Intrinsically disordered proteins or, regions perform important biological functions through their dynamic conformations during binding. Thus accurate identification of these disordered regions have significant implications in proper annotation of fu...
Intrinsically Disordered Proteins Crystallography, X-Ray Protein Structure, Secondary Area Under Curve Amino Acid Sequence Probability Datasets as Topic Algorithms ROC Curve Support Vector Machine
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Prediction Enhancement of Residue Real-Value Relative Accessible Surface Area in Transmembrane Helical Proteins by Solving the Output Preference Problem of Machine Learning-Based Predictors.

Journal of chemical information and modeling Oct 20, 2015
The α-helical transmembrane proteins constitute 25% of the entire human proteome space and are difficult targets in high-resolution wet-lab structural studies, calling for accurate computational predictors. We present a novel sequence-based method ca...
Solvents Protein Structure, Secondary Molecular Sequence Data Sequence Alignment Bacterial Proteins Amino Acid Sequence Solubility Protein Structure, Quaternary Succinate Dehydrogenase Wolinella Humans Machine Learning Animals Membrane Proteins Databases, Protein Models, Chemical
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Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

Immunogenetics Sep 29, 2015
A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented ...
Protein Binding Mice Computational Biology Cluster Analysis Databases, Protein Models, Molecular Peptide Fragments Humans Neural Networks, Computer Algorithms Animals Molecular Sequence Data Epitopes Sequence Homology, Amino Acid Amino Acid Sequence Histocompatibility Antigens Class II Binding Sites
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Correct machine learning on protein sequences: a peer-reviewing perspective.

Briefings in bioinformatics Sep 26, 2015
Machine learning methods are becoming increasingly popular to predict protein features from sequences. Machine learning in bioinformatics can be powerful but carries also the risk of introducing unexpected biases, which may lead to an overestimation ...
Machine Learning Humans Proteins Algorithms Amino Acid Sequence Computational Biology
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Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-Based Feature Descriptor.

Omics : a journal of integrative biology Sep 25, 2015
Proteins embody epitopes that serve as their antigenic determinants. Epitopes occupy a central place in integrative biology, not to mention as targets for novel vaccine, pharmaceutical, and systems diagnostics development. The presence of T-cell and ...
Epitopes, B-Lymphocyte Models, Statistical Amino Acid Sequence Datasets as Topic Molecular Sequence Data Humans Sensitivity and Specificity Software Computational Biology Support Vector Machine
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Knockdown of NADPH-cytochrome P450 reductase results in reduced resistance to buprofezin in the small brown planthopper, Laodelphax striatellus (fallén).

Pesticide biochemistry and physiology Sep 5, 2015
NADPH-cytochrome P450 reductase (CPR) plays an important role in cytochrome P450 function, and CPR knockdown in several insects leads to increased susceptibility to insecticides. However, a putative CPR gene has not yet been fully characterized in th...
NADPH-Ferrihemoprotein Reductase Sequence Homology, Amino Acid Cloning, Molecular Animals Thiadiazines Hemiptera Phylogeny Molecular Sequence Data Amino Acid Sequence Insecticide Resistance
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