AIMC Topic: Protein Interaction Domains and Motifs

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InterPred: A pipeline to identify and model protein-protein interactions.

Proteins Mar 21, 2017
Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the numb...
Software Molecular Docking Simulation Computational Biology Amino Acid Sequence Protein Interaction Mapping Sequence Analysis, Protein Protein Interaction Domains and Motifs Support Vector Machine Proteins Internet Benchmarking
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Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences.

BMC genomics Mar 14, 2017
BACKGROUND: The broad heterogeneity of antigen-antibody interactions brings tremendous challenges to the design of a widely applicable learning algorithm to identify conformational B-cell epitopes. Besides the intrinsic heterogeneity introduced by di...
Epitope Mapping Protein Interaction Domains and Motifs Epitopes, B-Lymphocyte Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Humans Supervised Machine Learning Protein Binding Antigens Models, Statistical Binding Sites B-Lymphocytes Antigen-Antibody Complex
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A Graph Approach to Mining Biological Patterns in the Binding Interfaces.

Journal of computational biology : a journal of computational molecular cell biology Nov 28, 2016
Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, ...
Computer Graphics Amino Acid Motifs Protein Interaction Domains and Motifs Computational Biology RNA-Binding Proteins Support Vector Machine Proteins Humans Data Mining Animals RNA Molecular Docking Simulation Protein Conformation Protein Binding Binding Sites
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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...
Humans Computer Simulation Animals Mice Models, Molecular Data Mining High-Throughput Nucleotide Sequencing Datasets as Topic Computational Biology Support Vector Machine Escherichia coli Proteins Gene Ontology Protein Interaction Mapping Protein Interaction Domains and Motifs Arabidopsis 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...
Protein Interaction Maps Proteins Databases, Protein Amino Acids Models, Biological Intrinsically Disordered Proteins Protein Interaction Mapping Protein Interaction Domains and Motifs Humans Machine Learning Animals
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Improved pan-specific prediction of MHC class I peptide binding using a novel receptor clustering data partitioning strategy.

HLA Oct 20, 2016
Pan-specific prediction of receptor-ligand interaction is conventionally done using machine-learning methods that integrates information about both receptor and ligand primary sequences. To achieve optimal performance using machine learning, dealing ...
Macaca Gorilla gorilla Pan troglodytes Epitopes Alleles Histocompatibility Antigens Class I Animals Ligands Oligopeptides Protein Binding Humans Binding Sites Mice Machine Learning Protein Interaction Domains and Motifs Gene Expression Software Structural Homology, Protein
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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...
Machine Learning Protein Processing, Post-Translational Proteins Protein Interaction Domains and Motifs
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OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.

Journal of computational biology : a journal of computational molecular cell biology Aug 11, 2016
In the two transmembrane protein types, outer membrane proteins (OMPs) perform diverse important biochemical functions, including substrate transport and passive nutrient uptake and intake. Hence their 3D structures are expected to reveal these funct...
Protein Conformation, beta-Strand Protein Structure, Tertiary Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Support Vector Machine Databases, Protein Biological Transport Bacterial Outer Membrane Proteins Membrane Lipids
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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...
Protein Conformation Protein Interaction Mapping Protein Interaction Domains and Motifs Humans Computational Biology Machine Learning Proteins Algorithms Databases, Protein
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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...
Gene Expression Profiling Support Vector Machine Humans Protein Interaction Maps Genetic Markers Protein Interaction Domains and Motifs Algorithms Models, Biological Gene Regulatory Networks Neoplasms Oligonucleotide Array Sequence Analysis Computational Biology
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