This detailed volume provides a comprehensive collection of classic and cutting-edge methods and techniques in mapping protein-protein interactions. The chapters include a variety of in vitro and in vivo experimental methods covering cell biology, biochemistry, and biophysics. In addition, the book also explores in silico methods including sequence-, structure-, and phylogenetic profile-based approaches as well as gene expression and machine learning methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists…mehr
This detailed volume provides a comprehensive collection of classic and cutting-edge methods and techniques in mapping protein-protein interactions. The chapters include a variety of in vitro and in vivo experimental methods covering cell biology, biochemistry, and biophysics. In addition, the book also explores in silico methods including sequence-, structure-, and phylogenetic profile-based approaches as well as gene expression and machine learning methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein-Protein Interactions: Methods and Protocols serves as an ideal guide for researchers working in protein science and beyond.
Yeast-Two-Hybrid Technique to Identify Protein-Protein Interactions.- Cytotrap: An Innovative Approach for Protein-Protein Interaction Studies for Cytoplasmic Proteins.- Analyzing Protein-Protein Interactions Using the Split-Ubiquitin System.- Detection of Protein-Protein Interactions Utilizing the Split-Ubiquitin Membrane-Based Yeast Two-Hybrid System.- Preparation and Utilization of a Versatile GFP-Protein Trap-Like System for Protein Complex Immunoprecipitation in Plants.- Tandem Affinity Purification (TAP) of Interacting Prey Proteins with FLAG- and HA-Tagged Bait Proteins.- Affinity Purification-Mass Spectroscopy (AP-MS) and Co-Immunoprecipitation (Co-IP) Technique to Study Protein-Protein Interactions.- Co-Immunoprecipitation-Based Identification of Effector-Host Protein Interactions from Pathogen-Infected Plant Tissue.- Co-Immunoprecipitation for Assessing Protein-Protein Interactions in Agrobacterium-Mediated Transient Expression System in Nicotiana benthamiana.-Detection of Protein-Protein Interactions Using Glutathione-S-Transferase (GST) Pull-Down Assay Technique.- Bimolecular Fluorescence Complementation (BiFC) Assay to Visualize Protein-Protein Interactions in Living Cells.- Detecting Protein-Protein Interactions Using Bimolecular Fluorescence Complementation (BiFC) and Luciferase Complementation Assays (LCA).- Forster Resonance Energy Transfer (FRET) to Visualize Protein-Protein Interactions in the Plant Cell.- Dynamic Proximity Tagging in Living Plant Cells with Pupylation-Based Interaction Tagging.- Characterization of Small Molecule-Protein Interactions Using SPR Method.- High-Throughput Protein-Protein Interactions Screening Using Pool-Based Liquid Yeast Two-Hybrid Pipeline.- Dynamic Enrichment for Evaluation of Protein Networks (DEEPN): A High Throughput Yeast Two-Hybrid (Y2H) Protocol to Evaluate Networks.- An Interactome Assay for Detecting Interactions between Extracellular Domains of Receptor Kinases.- Next-Generation YeastTwo-Hybrid Screening to Discover Protein-Protein Interactions.- Bioinformatic Analysis of Yeast Two-Hybrid Next-Generation Interaction Screen Data.- Discovering Protein-Protein Interactions Using Co-Fractionation-Mass Spectrometry with Label-Free Quantitation.- Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking (AP-CXL-MS) Proteomics.- Protein Interaction Screen on a Peptide Matrix (PrISMa).- Analyzing Protein Interactions by MAC-Tag Approaches.- Identification and Quantification of Affinity-Purified Proteins with MaxQuant, Followed by the Discrimination of Nonspecific Interactions with the CRAPome Interface.- Cataloguing Protein Complexes In Planta Using TurboID-Catalyzed Proximity Labeling.- A Data-Driven Signaling Network Inference Approach for Phosphoproteomics.- Pairwise and Multi-Chain Protein Docking Enhanced Using LZerD Web Server.- Predicting Protein Interaction Sites Using PITHIA.- Using PlaPPISite to Predict and Analyze Plant Protein-ProteinInteraction Sites.- Machine Learning Methods for Virus-Host Protein-Protein Interaction Prediction.- Protein-Protein Interaction Network Exploration Using Cytoscape.- Search, Retrieve, Visualize, and Analyze Protein-Protein Interactions from Multiple Databases: A Guide for Experimental Biologists.- Centrality Analysis of Protein-Protein Interaction Networks Using R.- Protein-Protein Interaction Network Analysis Using NetworkX.- Building Protein-Protein Interaction Graph Database Using Neo4j.
Yeast-Two-Hybrid Technique to Identify Protein-Protein Interactions.- Cytotrap: An Innovative Approach for Protein-Protein Interaction Studies for Cytoplasmic Proteins.- Analyzing Protein-Protein Interactions Using the Split-Ubiquitin System.- Detection of Protein-Protein Interactions Utilizing the Split-Ubiquitin Membrane-Based Yeast Two-Hybrid System.- Preparation and Utilization of a Versatile GFP-Protein Trap-Like System for Protein Complex Immunoprecipitation in Plants.- Tandem Affinity Purification (TAP) of Interacting Prey Proteins with FLAG- and HA-Tagged Bait Proteins.- Affinity Purification-Mass Spectroscopy (AP-MS) and Co-Immunoprecipitation (Co-IP) Technique to Study Protein-Protein Interactions.- Co-Immunoprecipitation-Based Identification of Effector-Host Protein Interactions from Pathogen-Infected Plant Tissue.- Co-Immunoprecipitation for Assessing Protein-Protein Interactions in Agrobacterium-Mediated Transient Expression System in Nicotiana benthamiana.-Detection of Protein-Protein Interactions Using Glutathione-S-Transferase (GST) Pull-Down Assay Technique.- Bimolecular Fluorescence Complementation (BiFC) Assay to Visualize Protein-Protein Interactions in Living Cells.- Detecting Protein-Protein Interactions Using Bimolecular Fluorescence Complementation (BiFC) and Luciferase Complementation Assays (LCA).- Forster Resonance Energy Transfer (FRET) to Visualize Protein-Protein Interactions in the Plant Cell.- Dynamic Proximity Tagging in Living Plant Cells with Pupylation-Based Interaction Tagging.- Characterization of Small Molecule-Protein Interactions Using SPR Method.- High-Throughput Protein-Protein Interactions Screening Using Pool-Based Liquid Yeast Two-Hybrid Pipeline.- Dynamic Enrichment for Evaluation of Protein Networks (DEEPN): A High Throughput Yeast Two-Hybrid (Y2H) Protocol to Evaluate Networks.- An Interactome Assay for Detecting Interactions between Extracellular Domains of Receptor Kinases.- Next-Generation YeastTwo-Hybrid Screening to Discover Protein-Protein Interactions.- Bioinformatic Analysis of Yeast Two-Hybrid Next-Generation Interaction Screen Data.- Discovering Protein-Protein Interactions Using Co-Fractionation-Mass Spectrometry with Label-Free Quantitation.- Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking (AP-CXL-MS) Proteomics.- Protein Interaction Screen on a Peptide Matrix (PrISMa).- Analyzing Protein Interactions by MAC-Tag Approaches.- Identification and Quantification of Affinity-Purified Proteins with MaxQuant, Followed by the Discrimination of Nonspecific Interactions with the CRAPome Interface.- Cataloguing Protein Complexes In Planta Using TurboID-Catalyzed Proximity Labeling.- A Data-Driven Signaling Network Inference Approach for Phosphoproteomics.- Pairwise and Multi-Chain Protein Docking Enhanced Using LZerD Web Server.- Predicting Protein Interaction Sites Using PITHIA.- Using PlaPPISite to Predict and Analyze Plant Protein-ProteinInteraction Sites.- Machine Learning Methods for Virus-Host Protein-Protein Interaction Prediction.- Protein-Protein Interaction Network Exploration Using Cytoscape.- Search, Retrieve, Visualize, and Analyze Protein-Protein Interactions from Multiple Databases: A Guide for Experimental Biologists.- Centrality Analysis of Protein-Protein Interaction Networks Using R.- Protein-Protein Interaction Network Analysis Using NetworkX.- Building Protein-Protein Interaction Graph Database Using Neo4j.
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