Chapters
Summary
Guidelines for computer based structural and functional characterization of protein using the I-TASSER pipeline is described. Starting from query protein sequence, 3D models are generated using multiple threading alignments and iterative structural assembly simulations. Functional inferences are thereafter drawn based on matches to proteins with known structure and functions.
Tags
Protocol Computer-based Protein Structure Function Prediction Genome Sequencing Projects Protein Sequence Structure And Function Knowledge Experimental Methods Computational Modeling I-TASSER Server Secondary Structure Prediction Solvent Accessibility Prediction Homologous Template Proteins Structure Alignments Tertiary Structural Models Structure-based Functional Annotations Confidence Score End Users User-specified Inter-residue Distance Contact Maps I-TASSER Modeling Template Proteins Structure Assembly Simulations
PLAYLIST
Cells and Genome
The Universal Features of Cells
The Diversity of Genomes and the Tree of Life
Genetic Information in Eukaryotes
Cell Chemistry and Biosynthesis
The Chemical Components of a Cell
Catalysis and the Use of Energy by Cells
How Cells Obtain Energy From Food
Proteins
The Shape and Structure of Proteins
Protein Function
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Research • BiologyA Protocol for Computer-Based Protein Structure and Function Prediction -
Research • BioengineeringStudying Protein Function and the Role of Altered Protein Expression by Antibody Interference and Three-dimensional Reconstructions -
Research • ChemistryBio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects
Basic Genetic Mechanisms
DNA, Chromosomes and Genomes
The Structure and Function of DNA
Chromosomal DNA and Its Packaging in the Chromatin Fiber
Chromatin Structure and Function
How Genomes Evolve
DNA Replication, Repair, and Recombination
The Maintenance of DNA Sequences
DNA Replication Mechanisms
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Education • Core: BiologyReplication in Eukaryotes -
Education • Core: BiologyReplication in Prokaryotes -
Research • BiochemistryProofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis -
Research • BiologyGenetic Studies of Human DNA Repair Proteins Using Yeast as a Model System -
Education • Core: BiologyProofreading
The Initiation and Completion Of DNA Replication in Chromosomes
Homologous Recombination
Transposition and Conservative Site Specific Recombination
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Research • BiologyAn Efficient In Vitro Transposition Method by a Transcriptionally Regulated Sleeping Beauty System Packaged into an Integration Defective Lentiviral Vector -
Research • BiologyPrinciples of Site-Specific Recombinase (SSR) Technology -
Education • Core: Molecular BiologyConservative Site-specific Recombination and Phase Variation -
Education • Core: Molecular BiologyOverview of Transposition and Recombination
How Cells Read the Genome: From DNA to Protein
From DNA to RNA
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Education • Core: BiologyTranscription -
Education • Core: BiologyTranscription Factors -
Education • Core: Molecular BiologyWhat is Gene Expression? -
Research • BioengineeringThe Encapsulation of Cell-free Transcription and Translation Machinery in Vesicles for the Construction of Cellular Mimics -
Research • GeneticsReal-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
From RNA to Protein
The RNA World and the Origins of Life
Control of Gene Expression
An Overview of Gene Control
Control of Transcription by Sequence- Specific DNA Binding Proteins
Molecular Genetic Mechanisms That Create and Maintain Specialized Cell Types
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Research • GeneticsAn Ecdysone Receptor-based Singular Gene Switch for Deliberate Expression of Transgene with Robustness, Reversibility, and Negligible Leakiness -
Education • Core: BiologyIntracellular Signaling Cascades -
Research • BiologyA Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents
Mechanisms That Reinforce Cell Memory in Plants and Animals
Post Transcriptional Controls
Regulation of Gene Expression By RNAs
Ways of Working With Cells
Analyzing Cells, Molecules and Systems
Isolating Cells and Growing Them in Culture
Purifying Proteins
Analyzing Proteins
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Education • Analytical ChemistryIon-Exchange Chromatography -
Education • Lab: ChemistryThin-Layer Chromatography- Concept -
Education • Lab: ChemistryColumn Chromatography- Concept -
Research • ChemistryAnalyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry -
Research • ChemistryAnalyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
Analyzing and Manipulating DNA
Studying Gene Expression and Function
Mathematical Analysis of Cell Functions
Visualizing Cells
Looking at Cells in the Light Microscope
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Education • General Laboratory TechniquesIntroduction to Light Microscopy -
Research • BiologyMajor Components of the Light Microscope -
Research • BiologyPhase Contrast and Differential Interference Contrast (DIC) Microscopy -
Education • ImmunologyConfocal Fluorescence Microscopy: A Technique to Determine the Localization of Proteins in Mouse Fibroblasts -
Research • ChemistryLuminescence Lifetime Imaging of O2 with a Frequency-Domain-Based Camera System -
Research • NeuroscienceIn Vivo Functional Brain Imaging Approach Based on Bioluminescent Calcium Indicator GFP-aequorin -
Research • BiologySample Preparation for Single Virion Atomic Force Microscopy and Super-resolution Fluorescence Imaging -
Education • Analytical ChemistryScanning Electron Microscopy (SEM) -
Research • EnvironmentSample Preparation Method of Scanning and Transmission Electron Microscope for the Appendages of Woodboring Beetle
Cells in Their Social Context
Cell Junctions, Cell Adhesion, and the Extracellular Matrix
Cell Cell Junctions
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Research • BioengineeringBead Aggregation Assays for the Characterization of Putative Cell Adhesion Molecules -
Research • Cancer ResearchStudying TGF-β Signaling and TGF-β-induced Epithelial-to-mesenchymal Transition in Breast Cancer and Normal Cells -
Research • Developmental BiologyImaging of Cell Shape Alteration and Cell Movement in Drosophila Gastrulation Using DE-cadherin Reporter Transgenic Flies -
Research • Developmental BiologyInduction of Mesenchymal-Epithelial Transitions in Sarcoma Cells -
Education • Core: BiologyMuscle Contraction -
Research • BiologyIsolation and Primary Culture of Rat Hepatic Cells
The Extracellular Matrix of Animals
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Education • Core: BiologyThe Extracellular Matrix -
Research • Cancer ResearchSynthesis and Characterization of Placental Chondroitin Sulfate A (plCSA)-Targeting Lipid-Polymer Nanoparticles -
Research • BioengineeringHyaluronic-Acid Based Hydrogels for 3-Dimensional Culture of Patient-Derived Glioblastoma Cells -
Research • BioengineeringOrganotypic Collagen I Assay: A Malleable Platform to Assess Cell Behaviour in a 3-Dimensional Context -
Research • Application Notes3D Tissue Engineered Systems for Regenerative Approaches, Drug Discovery, and Toxicity Screening - ADVERTISEMENT -
Research • BioengineeringPreparation of Extracellular Matrix Protein Fibers for Brillouin Spectroscopy -
Research • BioengineeringGenerating a Fractal Microstructure of Laminin-111 to Signal to Cells -
Research • BiochemistryGlycoproteomics of the Extracellular Matrix: A Method for Intact Glycopeptide Analysis Using Mass Spectrometry -
Research • Immunology and InfectionStatic Adhesion Assay for the Study of Integrin Activation in T Lymphocytes -
Research • BioengineeringImaging Integrin Tension and Cellular Force at Submicron Resolution with an Integrative Tension Sensor
The Plant Cell Wall
Cancer
Cancer as a Microevolutionary Process
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Education • Core: Molecular BiologyCancer Stem Cells and Tumor Maintenance -
Education • Core: Molecular BiologyThe Tumor Microenvironment -
Education • Core: Molecular BiologyCancers Originate from Somatic Mutations in a Single Cell -
Education • Core: BiologyCancer -
Education • Core: BiologyWhat is the Cell Cycle? -
Education • Lab BioCell Division- Concept
Cancer Critical Genes: How They Are Found and What They Do
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Education • Core: Molecular BiologyCancer-Critical Genes II: Tumor Suppressor Genes -
Education • Core: Molecular BiologyCancer-Critical Genes I: Proto-oncogenes -
Education • GeneticsAn Overview of Genetics and Disease -
Education • Core: Molecular BiologyTumor Progression -
Education • Core: Molecular BiologymTOR Signaling and Cancer Progression -
Education • Core: Molecular BiologyCanonical Wnt Signaling Pathway -
Education • Core: Molecular BiologyAdaptive Mechanisms in Cancer Cells -
Research • Cancer ResearchConditional Knockdown of Gene Expression in Cancer Cell Lines to Study the Recruitment of Monocytes/Macrophages to the Tumor Microenvironment -
Research • MedicineDNA Vector-based RNA Interference to Study Gene Function in Cancer
Cancer Prevention and Treatment: Present and Future
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Education • Core: Molecular BiologyCancer Prevention -
Education • Core: Molecular BiologyCancer Therapies -
Education • Core: Molecular BiologyTargeted Cancer Therapies -
Education • Core: Molecular BiologyTreatment Resistant Cancers -
Education • Core: Molecular BiologyCombination Therapies and Personalized Medicine
Development of Multicellular Organisms
Overview of Development
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Research • BiologyPharmacological and Functional Genetic Assays to Manipulate Regeneration of the Planarian Dugesia japonica -
Research • Developmental BiologyGeneration of Aggregates of Mouse Embryonic Stem Cells that Show Symmetry Breaking, Polarization and Emergent Collective Behaviour In Vitro -
Research • NeuroscienceSingle-cell Profiling of Developing and Mature Retinal Neurons
Mechanisms of Pattern Formation
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Education • Biology IDrosophila Development and Reproduction -
Research • MedicineA Protocol for Genetic Induction and Visualization of Benign and Invasive Tumors in Cephalic Complexes of Drosophila melanogaster -
Research • BiologyOptical Cross-Sectional Muscle Area Determination of Drosophila Melanogaster Adult Indirect Flight Muscles -
Research • NeuroscienceNovel Assay for Cold Nociception in Drosophila Larvae -
Research • GeneticsHOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
Developmental Timing
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Research • GeneticsAn Optogenetic Method to Control and Analyze Gene Expression Patterns in Cell-to-cell Interactions -
Research • BiologyGeneration of Dispersed Presomitic Mesoderm Cell Cultures for Imaging of the Zebrafish Segmentation Clock in Single Cells -
Research • BiologyChromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo
Morphogenesis
Neural Development
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Education • Core: BiologyLong-term Potentiation -
Research • NeuroscienceAn In Vitro Preparation for Eliciting and Recording Feeding Motor Programs with Physiological Movements in Aplysia californica -
Education • NeuroscienceAn Introduction to Developmental Neurobiology -
Education • NeuroscienceExplant Culture of Neural Tissue
