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Protein Interaction Domains and Motifs

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Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids.

International journal of molecular sciences 27792167
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...
Amino Acids Animals Databases, Protein Humans Intrinsically Disordered Proteins Machine Learning Models, Biological Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Interaction Maps Proteins
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Improved pan-specific prediction of MHC class I peptide binding using a novel receptor clustering data partitioning strategy.

HLA 27762504
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 ...
Alleles Animals Binding Sites Epitopes Gene Expression Gorilla gorilla Histocompatibility Antigens Class I Humans Ligands Macaca Machine Learning Mice Oligopeptides Pan troglodytes Protein Binding Protein Interaction Domains and Motifs Software Structural Homology, Protein
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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 27892693
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, ...
Amino Acid Motifs Animals Binding Sites Computational Biology Computer Graphics Data Mining Humans Molecular Docking Simulation Protein Binding Protein Conformation Protein Interaction Domains and Motifs Proteins RNA RNA-Binding Proteins Support Vector Machine
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Prediction of Protein-Protein Interactions by Evidence Combining Methods.

International journal of molecular sciences 27879651
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...
Animals Arabidopsis Computational Biology Computer Simulation Data Mining Datasets as Topic Drosophila melanogaster Escherichia coli Gene Ontology High-Throughput Nucleotide Sequencing Humans Mice Models, Molecular Molecular Sequence Annotation Protein Interaction Domains and Motifs Protein Interaction Mapping Proteins Saccharomyces cerevisiae Support Vector Machine
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An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions.

Methods in molecular biology (Clifton, N.J.) 28092029
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to ...
Algorithms Computational Biology Databases, Protein Humans Phosphotyrosine Protein Binding Protein Interaction Domains and Motifs Protein Interaction Mapping Reproducibility of Results Signal Transduction src Homology Domains Supervised Machine Learning Web Browser Workflow
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Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences.

BMC genomics 28361709
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...
Antigen-Antibody Complex Antigens B-Lymphocytes Binding Sites Epitope Mapping Epitopes, B-Lymphocyte Humans Models, Statistical Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Supervised Machine Learning
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InterPred: A pipeline to identify and model protein-protein interactions.

Proteins 28263438
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...
Amino Acid Sequence Benchmarking Computational Biology Internet Molecular Docking Simulation Protein Interaction Domains and Motifs Protein Interaction Mapping Proteins Sequence Analysis, Protein Software Support Vector Machine
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Editorial-Sequences and topology.

Current opinion in structural biology 28587734
Animals Binding Sites Computational Biology Humans Machine Learning Molecular Docking Simulation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Multimerization Proteins Thermodynamics
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Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules.

Immunology 28542831
MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or les...
Antibodies, Monoclonal Binding Sites Computational Biology Databases, Protein Epitopes Histocompatibility Antigens Class II Humans Ligands Machine Learning Mutation Neural Networks, Computer Peptides Protein Binding Protein Interaction Domains and Motifs Structure-Activity Relationship
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ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.

Bioinformatics (Oxford, England) 28130235
MOTIVATION: The identification of protein-protein interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational...
Computational Biology Machine Learning Protein Conformation Protein Interaction Domains and Motifs Sequence Analysis, Protein Software
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