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Protein Interaction Domains and Motifs

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Prediction of Protein-Protein Interactions by Evidence Combining Methods.

International journal of molecular sciences Nov 22, 2016
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of c...
Models, Molecular Data Mining High-Throughput Nucleotide Sequencing Datasets as Topic Support Vector Machine Escherichia coli Proteins Gene Ontology Protein Interaction Mapping Humans Protein Interaction Domains and Motifs Mice Arabidopsis Computational Biology Computer Simulation Animals Saccharomyces cerevisiae Drosophila melanogaster Molecular Sequence Annotation
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Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids.

International journal of molecular sciences Oct 26, 2016
Information about the interface sites of Protein-Protein Interactions (PPIs) is useful for many biological research works. However, despite the advancement of experimental techniques, the identification of PPI sites still remains as a challenging tas...
Humans Machine Learning Animals Protein Interaction Mapping Protein Interaction Domains and Motifs Amino Acids Models, Biological Protein Interaction Maps Intrinsically Disordered Proteins Proteins Databases, Protein
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GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

Proteins Sep 1, 2016
G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-d...
Humans Animals Models, Molecular Amino Acid Sequence Binding Sites Support Vector Machine Protein Interaction Domains and Motifs Databases, Protein Protein Structure, Secondary Receptors, G-Protein-Coupled Protein Multimerization Area Under Curve ROC Curve Protein Binding Mice
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Accurate contact predictions using covariation techniques and machine learning.

Proteins Sep 1, 2016
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...
Sequence Alignment Protein Interaction Domains and Motifs Software Computational Biology Internet Humans Databases, Protein Computer Simulation Amino Acid Sequence Neural Networks, Computer Viruses Models, Statistical Models, Molecular Bacteria Machine Learning Proteins Protein Structure, Secondary Protein Folding
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A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions.

BMC bioinformatics Aug 17, 2016
BACKGROUND: One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR ca...
Protein Interaction Domains and Motifs Machine Learning Protein Processing, Post-Translational Proteins
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A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.

International journal of molecular sciences Jul 27, 2016
Understanding protein-protein interactions is a key challenge in biochemistry. In this work, we describe a more accurate methodology to predict Hot-Spots (HS) in protein-protein interfaces from their native complex structure compared to previous publ...
Databases, Protein Protein Conformation Protein Interaction Mapping Protein Interaction Domains and Motifs Algorithms Computational Biology Proteins Humans Machine Learning
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Protein-protein interaction network construction for cancer using a new L1/2-penalized Net-SVM model.

Genetics and molecular research : GMR Jul 25, 2016
Identifying biomarker genes and characterizing interaction pathways with high-dimensional and low-sample size microarray data is a major challenge in computational biology. In this field, the construction of protein-protein interaction (PPI) networks...
Support Vector Machine Genetic Markers Models, Biological Protein Interaction Maps Humans Oligonucleotide Array Sequence Analysis Gene Regulatory Networks Protein Interaction Domains and Motifs Computational Biology Algorithms Neoplasms Gene Expression Profiling
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Protein-protein interaction inference based on semantic similarity of Gene Ontology terms.

Journal of theoretical biology Jul 21, 2016
Identifying protein-protein interactions is important in molecular biology. Experimental methods to this issue have their limitations, and computational approaches have attracted more and more attentions from the biological community. The semantic si...
Yeasts Molecular Sequence Annotation Gene Ontology Protein Interaction Mapping Protein Interaction Domains and Motifs Humans Machine Learning Support Vector Machine
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Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM.

Journal of biosciences Oct 1, 2015
Protein-protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown tha...
Humans Fuzzy Logic Escherichia coli Proteins Databases, Protein Protein Interaction Mapping Area Under Curve Sensitivity and Specificity Protein Interaction Domains and Motifs Support Vector Machine Gene Expression Escherichia coli
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