AIMC Topic: Sequence Analysis, Protein

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gkmSVM: an R package for gapped-kmer SVM.

Bioinformatics (Oxford, England) Apr 19, 2016
UNLABELLED: We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorith...
Algorithms Support Vector Machine Software Sequence Analysis, DNA Sequence Analysis, Protein
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PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.

Journal of molecular modeling Mar 11, 2016
The prediction of domain/linker residues in protein sequences is a crucial task in the functional classification of proteins, homology-based protein structure prediction, and high-throughput structural genomics. In this work, a novel consensus-based ...
Computational Biology Support Vector Machine Decision Trees Humans Neural Networks, Computer Structural Homology, Protein Caspase 10 Databases, Protein Protein Domains Caspase 8 Bayes Theorem Caspase 9 Discriminant Analysis Sequence Analysis, Protein
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A Web Server and Mobile App for Computing Hemolytic Potency of Peptides.

Scientific reports Mar 8, 2016
Numerous therapeutic peptides do not enter the clinical trials just because of their high hemolytic activity. Recently, we developed a database, Hemolytik, for maintaining experimentally validated hemolytic and non-hemolytic peptides. The present stu...
Internet Amino Acid Sequence Hemolysis Sequence Analysis, Protein Mobile Applications Humans Hemolytic Agents Computer Simulation Support Vector Machine Databases, Protein Peptides
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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...
Pattern Recognition, Automated Protein Structure, Secondary Molecular Sequence Data Databases, Protein Models, Chemical Amino Acid Sequence Sequence Analysis, Protein Machine Learning Algorithms Computer Simulation Membrane Proteins
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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....
Amino Acid Motifs Sequence Analysis, Protein Lysine Ubiquitin Ubiquitination Protein Domains Amino Acid Sequence Datasets as Topic Machine Learning Software Proteomics Proteome Mass Spectrometry Models, Molecular
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Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine.

PloS one Dec 4, 2015
The peptides derived from envelope proteins have been shown to inhibit the protein-protein interactions in the virus membrane fusion process and thus have a great potential to be developed into effective antiviral therapies. There are three types of ...
Viral Envelope Proteins Protein Binding Sequence Analysis, Protein Support Vector Machine Viral Fusion Protein Inhibitors Peptide Fragments
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A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Dec 3, 2015
BACKGROUND: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands...
Machine Learning Algorithms Molecular Docking Simulation Protein Binding Proteins Binding Sites Data Interpretation, Statistical Models, Chemical Protein Interaction Mapping Ligands Sequence Analysis, Protein Pattern Recognition, Automated
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Prediction the Substrate Specificities of Membrane Transport Proteins Based on Support Vector Machine and Hybrid Features.

IEEE/ACM transactions on computational biology and bioinformatics Nov 11, 2015
Membrane transport proteins and their substrate specificities play crucial roles in a variety of cellular functions. Identifying the substrate specificities of membrane transport proteins is closely related to the protein-target interaction predictio...
Substrate Specificity Protein Interaction Mapping Sequence Analysis, Protein Pattern Recognition, Automated Membrane Transport Proteins Protein Binding Binding Sites Support Vector Machine Models, Chemical Algorithms Molecular Docking Simulation
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Unsupervised learning assisted robust prediction of bioluminescent proteins.

Computers in biology and medicine Nov 10, 2015
Bioluminescence plays an important role in nature, for example, it is used for intracellular chemical signalling in bacteria. It is also used as a useful reagent for various analytical research methods ranging from cellular imaging to gene expression...
Algorithms Predictive Value of Tests Luminescent Proteins Sequence Analysis, Protein Machine Learning
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Computational probing protein-protein interactions targeting small molecules.

Bioinformatics (Oxford, England) Sep 28, 2015
MOTIVATION: With the booming of interactome studies, a lot of interactions can be measured in a high throughput way and large scale datasets are available. It is becoming apparent that many different types of interactions can be potential drug target...
Humans Protein Interaction Mapping Algorithms Sequence Analysis, Protein Support Vector Machine Drug Discovery Proteins Pharmaceutical Preparations
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