AIMC Topic: Sequence Analysis, Protein

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SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments.

Bioinformatics (Oxford, England) Feb 1, 2017
MOTIVATION: Chloroplasts are organelles found in plants and involved in several important cell processes. Similarly to other compartments in the cell, chloroplasts have an internal structure comprising several sub-compartments, where different protei...
Protein Transport Sequence Analysis, Protein Chloroplasts Computational Biology Membrane Proteins Plant Proteins Viridiplantae Machine Learning Software
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Learning Parameter-Advising Sets for Multiple Sequence Alignment.

IEEE/ACM transactions on computational biology and bioinformatics Jan 1, 2017
While the multiple sequence alignment output by an aligner strongly depends on the parameter values used for the alignment scoring function (such as the choice of gap penalties and substitution scores), most users rely on the single default parameter...
Computational Biology Sequence Alignment Sequence Analysis, Protein Machine Learning Algorithms
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Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix.

Oncotarget Dec 13, 2016
Self-interacting Proteins (SIPs) play an essential role in a wide range of biological processes, such as gene expression regulation, signal transduction, enzyme activation and immune response. Because of the limitations for experimental self-interact...
Fungal Proteins Support Vector Machine Protein Interaction Mapping Databases, Protein Sequence Analysis, Protein Humans Principal Component Analysis Position-Specific Scoring Matrices Computational Biology
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The importance of physicochemical characteristics and nonlinear classifiers in determining HIV-1 protease specificity.

Bioengineered Apr 2, 2016
This paper reviews recent research relating to the application of bioinformatics approaches to determining HIV-1 protease specificity, outlines outstanding issues, and presents a new approach to addressing these issues. Leading machine learning theor...
Support Vector Machine Amino Acid Sequence Sequence Analysis, Protein Artificial Intelligence Algorithms
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Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier.

IEEE/ACM transactions on computational biology and bioinformatics Jan 1, 2015
Predicting residues that participate in protein-protein interactions (PPI) helps to identify, which amino acids are located at the interface. In this paper, we show that the performance of the classical support vector machine (SVM) algorithm can furt...
Protein Interaction Mapping Molecular Sequence Data Sequence Alignment Pattern Recognition, Automated Binding Sites Sequence Analysis, Protein Computer Simulation Protein Binding Fuzzy Logic Models, Statistical Models, Chemical Amino Acid Sequence Humans Algorithms
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Sequence based human leukocyte antigen gene prediction using informative physicochemical properties.

International journal of data mining and bioinformatics Jan 1, 2015
Prediction of different classes within the human leukocyte antigen (HLA) gene family can provide insight into the human immune system and its response to viral pathogens. Therefore, it is desirable to develop an efficient and easily interpretable met...
HLA-A Antigens Leukocytes Support Vector Machine Pattern Recognition, Automated Humans Amino Acid Sequence Databases, Protein Molecular Sequence Data Algorithms Data Mining Structure-Activity Relationship Sequence Analysis, Protein
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Exploiting multi-layered vector spaces for signal peptide detection.

International journal of data mining and bioinformatics Jan 1, 2015
Analysing and classifying sequences based on similarities and differences is a mathematical problem of escalating relevance and importance in many scientific disciplines. One of the primary challenges in applying machine learning algorithms to sequen...
Peptides Support Vector Machine Databases, Protein Algorithms Protein Sorting Signals Molecular Sequence Data Amino Acid Sequence Sequence Alignment Data Mining Sequence Analysis, Protein Pattern Recognition, Automated
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Granular support vector machine to identify unknown structural classes of protein.

International journal of data mining and bioinformatics Jan 1, 2015
To date, classification of structural class using local protein structure rather than the whole structure has been gaining widespread attention. It is noted that the structural class lies in local composition or arrangement of secondary structure, wh...
Protein Structure, Secondary Sequence Analysis, Protein Support Vector Machine Proteins Databases, Protein Algorithms
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A novel fractal approach for predicting G-protein-coupled receptors and their subfamilies with support vector machines.

Bio-medical materials and engineering Jan 1, 2015
G-protein-coupled receptors (GPCRs) are seven membrane-spanning proteins and regulate many important physiological processes, such as vision, neurotransmission, immune response and so on. GPCRs-related pathways are the targets of a large number of ma...
Algorithms Support Vector Machine Databases, Protein Receptors, G-Protein-Coupled Sequence Alignment Sequence Analysis, Protein Fractals Data Mining Structure-Activity Relationship Pattern Recognition, Automated Amino Acid Sequence Molecular Sequence Data
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Sequence-based protein superfamily classification using computational intelligence techniques: a review.

International journal of data mining and bioinformatics Jan 1, 2015
Protein superfamily classification deals with the problem of predicting the family membership of newly discovered amino acid sequence. Although many trivial alignment methods are already developed by previous researchers, but the present trend demand...
Sequence Analysis, Protein Proteins Amino Acid Sequence Artificial Intelligence Algorithms Computational Biology
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