Proteopedia:Table of Contents

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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 to Structural Biology
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'''When you create a new page in Proteopedia, please add it to corresponding topic subpages.'''
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** Water
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*** [[Water in macromolecular models|Water in Macromolecular Models]]
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==Topics Pages Organized by Category==
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** Key Chemical Concepts for Structural Biology
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{{#tree:id=OrganizedByTopic|openlevels=0|
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* [[Introduction to protein structure]] - A introductory overview of protein structure.
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* [[About Macromolecular Structure]] - List of pages about macromolecular structure terms and concepts.
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* [[Proteopedia:Topic Pages|Topic pages]] - List of pages about specific proteins or protein families.
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* [[Index pages]] - List of pages that list other pages within Proteopedia.
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* Basics of Protein Structure
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**[[Introduction to protein structure]] - A introductory overview of protein structure
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**[[Proteins: primary and secondary structure]]
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**[[Myoglobin of Physeter catodon: structure]]
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** The Building Blocks
*** [[Amino Acids]]
*** [[Amino Acids]]
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*** [[Cation-pi interactions]]
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*** [[Backbone_representations]]
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*** [[Hydrogen bond]]
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*** [[Peptide]]
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*** [[Hydrogen_in_macromolecular_models|Hydrogen in Macromolecular Models]]
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**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
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*** [[Isoelectric_point]]
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**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
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* Biomolecules
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** Conformational flexibility of a polypeptide chain
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** [[About_Macromolecular_Structure]]
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*** [[Phi and Psi Angles]]
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*** [[Ramachandran Plots]]
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** Nucleotides, Nucleic Acids and Genetic Information
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*** [[Tutorial:Ramachandran principle and phi psi angles]]
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*** DNA
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** [[Secondary structure]]
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**** [[DNA]]
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*** [[Helices in Proteins]]
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**** B-DNA [[1bna]]
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**** [[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
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**** [[Z-DNA]]
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*** [[Sheets in Proteins]]
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**** [[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]]
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** Amino Acids
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** [[Structural_templates]]
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*** [[Amino_Acids]]
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*** [[Globular_Proteins]]
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*** [[Selenocysteine]]
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**** [[Turns in Proteins]]
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** Proteins, Primary Structure
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*** [[Fibrous Proteins]]
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*** [[Conservation,_Evolutionary]]
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*** [[Isoelectric_point]]
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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 structural motifs
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**** [[User:James_D_Watson/Structural_Templates]]
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*** Fibrous Proteins
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**** [[Coiled_coil]]
**** [[Coiled_coil]]
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**** [[Collagen]]
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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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*** Protein Misfolding
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**** [[Fibroins]]
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**** [[Prion_protein]]
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**** [[A_Physical_Model_of_the_Structure_of_GNNQQNY_from_Yeast_Prion_Sup35]]
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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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** [[Unusual Motifs in Proteins]]
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*** [[Helix-turn-helix motif]]
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*** [[Cation-pi_interactions]]
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*** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]
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*** [[Thermal_motion_of_peptide]]
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** Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
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** [[Intrinsically Disordered Protein]]
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*** Antibodies
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**** [[IgA]]
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**** [[Epitopes]]
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**** [[Major_Histocompatibility_Complex_Class_I]]
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*** [[Calmodulin_in_motion]]
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*** [[Myoglobin]]
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*** [[Hemoglobin]]; [[Hemoglobin_(Hebrew)]]
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*** [[Kinesin-5]]
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** Lipids and Biological Membranes
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** Lipid Binding Proteins
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*** [[CRABP_I_(_Cellular_Retinoic_Acid_Binding_Protein_)]]
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** Membrane Transport Proteins
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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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*** [[Ion_channels]]
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**** [[M2_Proton_Channel]]
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**** [[Voltage-gated_calcium_channels]]
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*** [[Mechanosensitive_channels:_opening_and_closing]]
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***[[Enzyme_I_of_the_Phosphoenolpyruvate:Sugar_Phosphotransferase_System]]
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** Prions and Intrinsically Disordered Proteins
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* Carbohydrates
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*** [[Prion_protein]]
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**[[Carbohydrates]]
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*** [[Doppel]]
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**[[Carbohydrates II]]
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*** [[Intrinsically Disordered Protein]]
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* Cytoskeletal Proteins
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** [[Actin]]
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** [[Keratins]]
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** [[Tropomyosin]]
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** [[Tubulin]]
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** Toxins
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* Lipids
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*** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
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**[[Lipids: structure and classification]]
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** Mitosis, Meiosis and Cargo Transport Proteins
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* Diseases & Related Topics
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*** [[Kinesin-5]]
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** [[Alzheimer's Disease]]
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** [[Antibody]]
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** Viruses
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** [[Bacterial Infections]]
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*** [[User:Wayne_Decatur/Suppression_of_RNA_Silencing_by_Viruses]]
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** [[Cancer]]
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*** Filamentous bacteriphage
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** [[Coronavirus Disease 2019 (COVID-19)]]
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**** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage
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** [[Diabetes & Hypoglycemia]]
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*** HIV
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** [[Hemophilia]]
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**** [[HIV-1 protease]]
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** [[HIV]]
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**** [[HIV-1 Gag]]
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** [[Hypertension & Congestive Heart Failure]]
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**** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
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** [[Immune Response]]
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**** [[User:Eric_Martz/Molecular_Playground/HIVDrug]]
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** [[Inflammation & Rheumatoid Arthritis]]
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*** Herpes Simplex Virus
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** [[Influenza]]
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**** [[Herpes_Simplex_Virus_Thymidine_Kinase]]
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** [[Metabolic Disorders]]
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*** Influenza
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** [[Neurodevelopmental Disorders]]
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**** [[Influenza_hemagglutinin]]
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** [[Oncogenes]]
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**** [[Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza]]
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** [[Pharmaceutical Drugs]]
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** [[Pharmaceutical Drug Targets]]
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** [[Toxins]]
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** [[Viral Infections]]
* Enzymes
* Enzymes
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** Enzymatic Catalysis
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** [[Hydrolases]]
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*** Acid-beta-glucosidase
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** [[Isomerases]]
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**** reHuman Acid-beta-glucosidase made in CHO cells [[1ogs]]
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** [[Ligases]]
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**** reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide [[1y7v]]
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** [[Lyases]]
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**** reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin [[2v3d]]
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** [[Oxidoreductases]]
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**** Velaglucerase Alfa [[2wkl]]
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** [[Transferases]]
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*** Acid Proteases
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**** [[HIV-1 protease]]
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**** [[Streptomyces_griseus_Aminopeptidase_(SGAP)]]; [[Aminopeptidase]]
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* Gene Expression & Replication
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*** [[Aconitase]]
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** [[DNA Replication]]
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*** Cysteine Proteases
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** [[Nucleic Acids]]
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*** [[Hen Egg-White (HEW) Lysozyme]]
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** [[Regulation of Gene Expression]]
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*** [[Choline_Oxidase]]
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** [[RNAi]]
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*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
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** [[Transcription & RNA Processing]]
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*** Metaloproteases
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** [[Translation]]
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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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*** [[Phosphofructokinase_%28PFK%29]]
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*** [[Pyruvate_phosphate_dikinase]]
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*** [[Serotonin_N-acetyltransferase]]
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*** Serine Hydrolases
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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 (Arabic)]]; [[1eve (Chinese)]]; [[1eve (Italian)]]; [[1eve (Russian)]]; [[1eve (Spanish)]]; [[1eve (Turkish)]]
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****** [[AChE_bivalent_inhibitors]]
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**** [[Tobacco_Etch_Virus_(TEV)_Protease]]
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*** [[Serine_Protease]]
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**** [[Trypsin]]
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*** [[Triose_Phosphate_Isomerase]]
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** Enzyme Inhibitors
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*** [[Alpha-1-antitrypsin]]
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** Enzyme Kinetics, Inhibition, and Control
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***[[Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza]]
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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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*** [[Bcl-2]]
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*** [[C-Myc]]
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** Enzymes - Molecular Machines
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*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
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*** [[Pyruvate phosphate dikinase]]
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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]]
* Metabolism
* Metabolism
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** Introduction to 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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** Glucose Catabolism
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* Miscellaneous
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*** [[Triose_Phosphate_Isomerase]]
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** [[Colored & Bioluminescent Proteins]]
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***[[Phosphofructokinase_%28PFK%29]]
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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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** Glycogen Metabolism and Gluconeogenesis
 
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*** [[Phosphoglucose_isomerase]]
 
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*** [[Calmodulin_in_motion]]
 
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*** [[Biotin_Protein_Ligase]]
 
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** Citric Acid Cycle
 
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*** [[Aconitase]]
 
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** Electron Transport and Oxidative Phosphorylation
 
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*** [[NADH quinone oxidoreductase ]]
 
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** Photosynthesis
 
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*** [[Photosystem_II]]
 
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*** [[Ribulose-1,5-bisphosphate_carboxylase/oxygenase]]
 
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*** [[PrrA_in_Rhodobacter_sphaeroides]]
 
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*** [[Pyruvate_phosphate_dikinase]]
 
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** Lipid Metabolism
 
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*** [[Acid-beta-glucosidase]]
 
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** Amino Acid Metabolism
 
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*** [[Aromatic_amino_acid_hydroxylases]]
 
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*** [[Phenylalanine_hydroxylase]]
 
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*** [[Tyrosine_hydroxylase]]
 
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*** [[ATP_Phosphoribosyl_Transferase]]
 
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*** [[Isochorismate_pyruvate_lyase]]
 
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** Mammalian Fuel Metabolism: Integration and Regulation
 
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** Nucleotide Metabolism
 
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*** [[Dihydrofolate_reductase]]
 
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* Gene Expression and Replication
 
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** Nucleic Acid Structure
 
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*** [[DNA]]
 
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**** B-DNA [[1bna]]
 
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**** [[Z-DNA]]
 
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*** [[Nucleosomes]]
 
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** DNA Replication, Repair, and Recombination
 
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*** [[DNA Replication,Transcription and Translation]]
 
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*** [[DNA_Polymerase_I]]
 
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*** [[PcrA_helicase]]
 
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*** [[Fpg_Nei_Protein_Superfamily]] - DNA Repair and Base Excision DNA Repair
 
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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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*** [[Structure_of_E._coli_DnaC_helicase_loader]]
 
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***[[1x9n#Crystal_Structure_of_Human_DNA_Ligase_I_bound_to_5.27-adenylated.2C_nicked_DNA]]
 
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*** [[Rop_protein]]
 
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** Transcription and RNA Processing
 
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*** [[C-Myc]]
 
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*** [[Lac_repressor]]
 
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*** [[Reverse_transcriptase]]
 
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*** [[TATA-Binding_Protein]]
 
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*** [[RSP1275]]
 
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*** [[Transcription_Termination_Factor_Rho]]
 
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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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*** [[Lac_repressor]]
 
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*** [[Irr]]
 
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*** Oncogenes
 
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**** [[P53]]
 
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**** [[SRC]]
 
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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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** Antibodies
 
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*** [[IgA]]
 
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*** [[Epitopes]]
 
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** [[Major_Histocompatibility_Complex_Class_I]]
 
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*** [[Human_beta_two_microglobulin]]
 
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* Diseases
 
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** Cancer
 
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*** [[SRC]]
 
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*** [[Proteins involved in cancer]]
 
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* Methods of Structure Determination
 
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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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** Structural Analysis & Visualization
 
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*** [[CPK]] - Corey-Pauling-Koltun spacefilling molecular models and color scheme for elements
 
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*** [[Chime]]
 
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*** Jmol
 
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**** [[S347/Visualising_protein_structure|Visualising Protein Structure]] - Introduction to Jmol
 
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**** [[FirstGlance_in_Jmol]]
 
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*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
 
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*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
 
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*** Homology Model
 
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**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
 
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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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*** [[DRuMS]] - set of standard color schemes for macromolecular visualization
 
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** Sequence Analysis
 
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*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]
 
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* Model Structures
 
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** [[African_Malaria_Mosquito_Acetylcholinesterase]]
 
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* Miscellaneous
 
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** [[Molecular_Playground]]
 
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** [[Research Groups]]
 
}}
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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



Retrieved from "http://52.214.119.220/wiki/index.php/Proteopedia:Table_of_Contents"
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