AIMC Topic: Sequence Analysis, Protein

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KeBABS: an R package for kernel-based analysis of biological sequences.

Bioinformatics (Oxford, England) Mar 25, 2015
KeBABS provides a powerful, flexible and easy to use framework for KE: rnel- B: ased A: nalysis of B: iological S: equences in R. It includes efficient implementations of the most important sequence kernels, also including variants that allow for tak...
Software Algorithms Computer Simulation Humans Artificial Intelligence Peptide Fragments HLA-A2 Antigen Sequence Analysis, Protein Models, Theoretical Support Vector Machine
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Prediction of cancer proteins by integrating protein interaction, domain frequency, and domain interaction data using machine learning algorithms.

BioMed research international Mar 17, 2015
Many proteins are known to be associated with cancer diseases. It is quite often that their precise functional role in disease pathogenesis remains unclear. A strategy to gain a better understanding of the function of these proteins is to make use of...
Neoplasms Algorithms Humans Databases, Protein Animals Neoplasm Proteins Machine Learning Protein Structure, Tertiary Sequence Analysis, Protein
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Prediction and analysis of quorum sensing peptides based on sequence features.

PloS one Mar 17, 2015
Quorum sensing peptides (QSPs) are the signaling molecules used by the Gram-positive bacteria in orchestrating cell-to-cell communication. In spite of their enormous importance in signaling process, their detailed bioinformatics analysis is lacking. ...
Bacteria Sequence Analysis, Protein Software Support Vector Machine Bacterial Proteins Peptides Quorum Sensing
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Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.

BMC systems biology Feb 6, 2015
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
Protein Conformation Computational Biology Nucleic Acid Conformation Support Vector Machine Sequence Analysis, Protein DNA-Binding Proteins Molecular Sequence Data Models, Molecular Amino Acid Sequence Internet
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More challenges for machine-learning protein interactions.

Bioinformatics (Oxford, England) Jan 12, 2015
MOTIVATION: Machine learning may be the most popular computational tool in molecular biology. Providing sustained performance estimates is challenging. The standard cross-validation protocols usually fail in biology. Park and Marcotte found that even...
Humans Sequence Analysis, Protein Artificial Intelligence Protein Interaction Mapping Proteins Computational Biology Saccharomyces cerevisiae Proteins
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A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets.

Molecular informatics Jan 8, 2015
Improved understanding of the forces that determine drug specificity to their targets is important for drug design and discovery, as well as for gaining knowledge about molecular recognition. Here, we present a machine learning approach that includes...
Machine Learning Sequence Analysis, Protein Membrane Proteins
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GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.

Bioinformatics (Oxford, England) Jan 6, 2015
MOTIVATION: Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes (BPs) such as cellular communication, ligand recognition and subcellular reco...
Sequence Analysis, Protein Protein Processing, Post-Translational Amino Acids Proteome Glycosylation Humans Software Algorithms Artificial Intelligence
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Identification of human drug targets using machine-learning algorithms.

Computers in biology and medicine Nov 20, 2014
Identification of potential drug targets is a crucial task in the drug-discovery pipeline. Successful identification of candidate drug targets in entire genomes is very useful, and computational prediction methods can speed up this process. In the cu...
Humans Artificial Intelligence Drug Delivery Systems Sequence Analysis, Protein Algorithms
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Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine.

Journal of theoretical biology Oct 22, 2014
β-Lactam class of antibiotics is used as major therapeutic agent against a number of pathogenic microbes. The widespread and indiscriminate use of antibiotics to treat bacterial infection has prompted evolution of several evading mechanisms from the ...
beta-Lactamases Protein Structure, Secondary Support Vector Machine Amino Acid Sequence Sequence Analysis, Protein beta-Lactams Anti-Infective Agents
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Discrimination of acidic and alkaline enzyme using Chou's pseudo amino acid composition in conjunction with probabilistic neural network model.

Journal of theoretical biology Oct 22, 2014
Enzyme catalysis is one of the most essential and striking processes among of all the complex processes that have evolved in living organisms. Enzymes are biological catalysts, which play a significant role in industrial applications as well as in me...
Neural Networks, Computer Algorithms Databases, Protein Enzymes Sequence Analysis, Protein Models, Chemical Protein Folding
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