Proteopedia:Table of Contents

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{{#tree:id=siteTree|openlevels=1|root='''Chemistry of Life'''|close=top|open=top|
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This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the [[Help:Searching|search slots at the left]] if you don't find what you are looking for below. Updated: {{REVISIONDAY2}}-{{REVISIONMONTH}}-{{REVISIONYEAR}} (DD-MM-YYYY)
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* INTRODUCTION
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'''When you create a new page in Proteopedia, please add it to corresponding topic subpages.'''
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** Introduction to the Chemistry of Life
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** Water
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*** [[Water_in_macromolecular_models|Water in Macromolecular Models]]
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** Key chemical concepts for Structural Biology
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*** [[Cation-pi interactions]]
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*** [[Hydrogen bond]]
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*** [[Hydrogen_in_macromolecular_models|Hydrogen in Macromolecular Models]]
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* BIOMOLECULES
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==Topics Pages Organized by Category==
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** Nucleotides, Nucleic Acids, and Genetic Information
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*** [[DNA]]
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**** [[Z-DNA]]
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** [[Amino_Acids]]
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***[[Selenocysteine]]
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** Proteins: Primary Structure
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** Proteins: Three-Dimensional Structure
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*** [[S347/The four tiers of protein structure]]
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***[[Secondary_structure]]
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*** Protein Misfolding
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****[[Prion_protein]]
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** Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
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*** Antibodies
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**** [[IgA]]
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**** [[Epitopes]]
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*** [[Calmodulin_in_motion]]
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*** [[Collagen]]
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*** [[Hemoglobin]]; [[Hemoglobin_(Hebrew)]]
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** COLORED PROTEINS & THOSE THAT CHANGE COLOR
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*** [[Green Fluorescent Protein]]; [[GFP_(Hebrew)]]
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*** [[Dronpa]]
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*** [[Factor IX]]
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** DNA BINDING PROTEINS
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*** [[Helix-turn-helix motif]]
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*** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]
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** Lipids and Biological Membranes
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** Membrane Transport
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*** [[A Physical Model of the β2-Adrenergic Receptor]]
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***[[Lactose_Permease]]
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***[[Proton_Channels]]
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***[[Mechanosensitive_channels:_opening_and_closing]]
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** Prions & Intrinsically Disordered Proteins
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*** [[Doppel]]
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*** [[Intrinsically Disordered Protein]]
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** Toxins
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*** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
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** Viruses
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*** Filamentous bacteriphage
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**** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage
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*** HIV
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**** [[HIV-1 protease]]
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**** [[HIV-1 Gag]]
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**** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
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*** Herpes Simplex Virus
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**** [[Herpes_Simplex_Virus_Thymidine_Kinase]]
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*** Influenzan
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**** [[Influenza_hemagglutinin]]
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* ENZYMES
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** Enzymatic Catalysis
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*** [[Aconitase]]
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*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
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*** Serine Hydrolases
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****[[Serine_Protease]]
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**** [[Acetylcholinesterase]] (AChE)
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***** [[Acetylcholine]]
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***** [[Flexibility_of_aromatic_residues_in_acetylcholinesterase]]
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***** [[AChE inhibitors and substrates]]
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****** [[1eve]] AChE-Aricept complex; [[1eve (Chinese)]]; [[1eve (Russian)]]; [[1eve (Spanish)]]; [[1eve (Turkish)]]
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****** [[AChE_bivalent_inhibitors]]
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***[[Triose_Phosphate_Isomerase]]
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***[[Pyruvate_phosphate_dikinase]]
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***Cysteine Proteases
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****[[Tobacco_Etch_Virus_(TEV)_Protease]]
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****[[Streptomyces_griseus_Aminopeptidase_(SGAP)]]
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***Acid Proteases
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****[[HIV-1 protease]]
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****[[Pepsin]]
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***Metaloproteases
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****[[Metalloproteases]]
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****[[Matrix_metalloproteinases]]
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***Oxidoreductases
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****[[NADH quinone oxidoreductase ]]
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** Enzyme Kinetics, Inhibition, and Control
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** Biochemical Signaling
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***[[Nitric_oxide_synthase]]
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***[[Recoverin,_a_calcium-activated_myristoyl_switch]]
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* METABOLISM
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* [[Introduction to protein structure]] - A introductory overview of protein structure.
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** Introduction to Metabolism
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* [[About Macromolecular Structure]] - List of pages about macromolecular structure terms and concepts.
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** Glucose Catabolism
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* [[Proteopedia:Topic Pages|Topic pages]] - List of pages about specific proteins or protein families.
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***[[Triose_Phosphate_Isomerase]]
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* [[Index pages]] - List of pages that list other pages within Proteopedia.
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** Glycogen Metabolism and Gluconeogenesis
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* Basics of Protein Structure
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*** [[Phosphoglucose_isomerase]]
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**[[Introduction to protein structure]] - A introductory overview of protein structure
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** Citric Acid Cycle
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**[[Proteins: primary and secondary structure]]
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** Electron Transport and Oxidative Phosphorylation
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**[[Myoglobin of Physeter catodon: structure]]
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***[[NADH quinone oxidoreductase ]]
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** The Building Blocks
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** Photosynthesis
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*** [[Amino Acids]]
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***[[Photosystem_II]]
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*** [[Backbone_representations]]
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***[[Ribulose-1,5-bisphosphate_carboxylase/oxygenase]]
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*** [[Peptide]]
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***[[PrrA_in_Rhodobacter_sphaeroides]]
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**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
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***[[Pyruvate_phosphate_dikinase]]
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**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
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** Lipid Metabolism
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** Amino Acid Metabolism
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***[[Phenylalanine_hydroxylase]]
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** Mammalian Fuel Metabolism: Integration and Regulation
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* GENE EXPRESSION AND REPLICATION
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** Conformational flexibility of a polypeptide chain
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** Nucleotide Metabolism
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*** [[Phi and Psi Angles]]
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** Nucleic Acid Structure
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*** [[Ramachandran Plots]]
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***[[Z-DNA]]
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*** [[Tutorial:Ramachandran principle and phi psi angles]]
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***[[Nucleosomes]]
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** [[Secondary structure]]
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** DNA Replication, Repair, and Recombination
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*** [[Helices in Proteins]]
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*** [[DNA Replication,Transcription and Translation]]
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**** [[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
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***{[PcrA_helicase]}
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*** [[Sheets in Proteins]]
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*** [[Fpg_Nei_Protein_Superfamily]] - DNA Repair and Base Excision DNA Repair
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**** [[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]]
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*** [[Human RecQ-Like protein 1]] - RecQ family of DNA helicases are conserved in from bacteria to man
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** [[Structural_templates]]
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***[[Structure_of_E._coli_DnaC_helicase_loader]]
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*** [[Globular_Proteins]]
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***[[Rop_protein]]
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**** [[Turns in Proteins]]
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** Transcription and RNA Processing
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*** [[Fibrous Proteins]]
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***[[TATA-Binding_Protein]]
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**** [[Coiled_coil]]
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***[[RSP1275]]
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**** [[Collagen]] - Illustrates the structure of a collagen segment as well as the structure of a mutated tropocollagen.
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***[[Transcription_Termination_Factor_Rho]]
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**** [[Fibroins]]
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** Protein Synthesis
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***[[Ribosome]]
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***[[SelB_Recognition]]
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** Regulation of Gene Expression
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***[[Tangible_Models_of_Cdc42_Interacting_With_Intersectin]]
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* EVOLUTION
 
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** [[Conservation, Evolutionary]]
 
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** [[Extremophiles]]
 
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*IMMUNE SYSTEM
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** [[Unusual Motifs in Proteins]]
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**[[Major_Histocompatibility_Complex_Class_I]]
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*** [[Cation-pi_interactions]]
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*** [[Thermal_motion_of_peptide]]
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* METHODS OF STRUCTURE DETERMINATION
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** [[Intrinsically Disordered Protein]]
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** X-ray
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***[[X-ray_crystallography]]
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****[[Asymmetric_Unit]]
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****[[Biological_Unit]]
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****[[Electron_density_maps]]
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***SAXS
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** NMR
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***[[NMR_Ensembles_of_Models]]
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** Electron Microscopy
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* METHODS OF STRUCTURE & SEQUENCE ANALYSIS
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* Carbohydrates
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** STRUCTURAL ANALYSIS & VISUALIZATION
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**[[Carbohydrates]]
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*** [[Chime]]
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**[[Carbohydrates II]]
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*** Jmol
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* Cytoskeletal Proteins
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**** [[S347/Visualising_protein_structure|Visualising Protein Structure]] - Introduction to Jmol
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** [[Actin]]
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**** [[FirstGlance_in_Jmol]]
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** [[Keratins]]
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*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
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** [[Tropomyosin]]
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*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
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** [[Tubulin]]
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*** Homology Model
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**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
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* Lipids
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**** [[User:Emi Nakayama/TRIM5a Homology Models|TRIM5a Homology Models]] - Differences in models as a function of their templates
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**[[Lipids: structure and classification]]
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*** [[DRuMS]] - set of standard color schemes for macromolecular visualization
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** SEQUENCE ANALYSIS
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* Diseases & Related Topics
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*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]
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** [[Alzheimer's Disease]]
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** [[Antibody]]
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** [[Bacterial Infections]]
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** [[Cancer]]
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** [[Coronavirus Disease 2019 (COVID-19)]]
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** [[Diabetes & Hypoglycemia]]
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** [[Hemophilia]]
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** [[HIV]]
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** [[Hypertension & Congestive Heart Failure]]
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** [[Immune Response]]
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** [[Inflammation & Rheumatoid Arthritis]]
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** [[Influenza]]
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** [[Metabolic Disorders]]
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** [[Neurodevelopmental Disorders]]
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** [[Oncogenes]]
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** [[Pharmaceutical Drugs]]
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** [[Pharmaceutical Drug Targets]]
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** [[Toxins]]
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** [[Viral Infections]]
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* Enzymes
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** [[Hydrolases]]
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** [[Isomerases]]
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** [[Ligases]]
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** [[Lyases]]
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** [[Oxidoreductases]]
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** [[Transferases]]
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* Gene Expression & Replication
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** [[DNA Replication]]
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** [[Nucleic Acids]]
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** [[Regulation of Gene Expression]]
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** [[RNAi]]
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** [[Transcription & RNA Processing]]
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** [[Translation]]
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* Large Macromolecular Assemblies
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** [[Group:MUZIC|Muscle sarcomere: Z-Disk]]
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** [[Ribosome]]
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** [[Ribosoma 70S]]
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** [[Nucleosomes]]
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** [[Nucleosome structure]]
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* Metabolism
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** [[Amino Acid Synthesis & Metabolism]]
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** [[Carbohydrate Metabolism]]
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** [[Photosynthesis]]
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** [[Regulation of Gene Expression]]
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** [[Drug Metabolism by CYP450 Enzymes]]
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* Miscellaneous
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** [[Colored & Bioluminescent Proteins]]
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** [[Coronavirus Disease 2019 (COVID-19)]]
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** [[Enzimas: complejo enzima-sustrato]]
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** [[3D Molecular Models]]
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* Signaling & Transport
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** [[Hormone]]
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** [[Membrane Channels & Pumps]]
}}
}}
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__NOTOC__
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__NOEDITSECTION__

Current revision

This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the search slots at the left if you don't find what you are looking for below. Updated: 30-12-2021 (DD-MM-YYYY)

When you create a new page in Proteopedia, please add it to corresponding topic subpages.

Topics Pages Organized by Category



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