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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***[[Isoelectric_point]]
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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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**** [[DNA]]
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****B-DNA [[1bna]]
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**** [[Z-DNA]]
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**AMINO ACIDS
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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 structural motifs
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****[[User:James_D_Watson/Structural_Templates]]
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***FIBROUS PROTEINS
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****[[Coiled_coil]]
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**** [[Collagen]]
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*** Protein Misfolding
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****[[Prion_protein]]
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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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** 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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****[[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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* [[Introduction to protein structure]] - A introductory overview of protein structure.
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** MEMBRANE TRANSPORT PROTEINS
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* [[About Macromolecular Structure]] - List of pages about macromolecular structure terms and concepts.
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*** [[A Physical Model of the β2-Adrenergic Receptor]]
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* [[Proteopedia:Topic Pages|Topic pages]] - List of pages about specific proteins or protein families.
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***[[Lactose_Permease]]
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* [[Index pages]] - List of pages that list other pages within Proteopedia.
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***[[Proton_Channels]]
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* Basics of Protein Structure
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***[[Ion_channels]]
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**[[Introduction to protein structure]] - A introductory overview of protein structure
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***[[Mechanosensitive_channels:_opening_and_closing]]
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**[[Proteins: primary and secondary structure]]
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**PRIONS AND INTRINSICALLY DISORDERED PROTEINS
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**[[Myoglobin of Physeter catodon: structure]]
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***[[Prion_protein]]
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** The Building Blocks
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*** [[Doppel]]
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*** [[Amino Acids]]
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*** [[Intrinsically Disordered Protein]]
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*** [[Backbone_representations]]
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** TOXINS
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*** [[Peptide]]
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*** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
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**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
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**MITOSIS, MEOSIS, AND CARGO TRANSPORT PROTEINS
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**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
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***[[Kinesin-5]]
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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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*** Influenza
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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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** Conformational flexibility of a polypeptide chain
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** Introduction to Metabolism
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*** [[Phi and Psi Angles]]
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** Glucose Catabolism
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*** [[Ramachandran Plots]]
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***[[Triose_Phosphate_Isomerase]]
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*** [[Tutorial:Ramachandran principle and phi psi angles]]
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** Glycogen Metabolism and Gluconeogenesis
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** [[Secondary structure]]
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*** [[Phosphoglucose_isomerase]]
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*** [[Helices in Proteins]]
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*** [[Calmodulin_in_motion]]
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**** [[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
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** Citric Acid Cycle
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*** [[Sheets in Proteins]]
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** Electron Transport and Oxidative Phosphorylation
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**** [[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]]
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***[[NADH quinone oxidoreductase ]]
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** [[Structural_templates]]
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** Photosynthesis
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*** [[Globular_Proteins]]
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***[[Photosystem_II]]
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**** [[Turns in Proteins]]
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***[[Ribulose-1,5-bisphosphate_carboxylase/oxygenase]]
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*** [[Fibrous Proteins]]
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***[[PrrA_in_Rhodobacter_sphaeroides]]
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**** [[Coiled_coil]]
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***[[Pyruvate_phosphate_dikinase]]
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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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** Lipid Metabolism
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**** [[Fibroins]]
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** Amino Acid Metabolism
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***[[Phenylalanine_hydroxylase]]
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***[[Isochorismate_pyruvate_lyase]]
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** Mammalian Fuel Metabolism: Integration and Regulation
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* GENE EXPRESSION AND REPLICATION
 
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** Nucleotide Metabolism
 
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** Nucleic Acid Structure
 
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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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***{[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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***[[Rop_protein]]
 
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** Transcription and RNA Processing
 
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***[[Lac_repressor]]
 
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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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***[[Tangible_Models_of_Cdc42_Interacting_With_Intersectin]]
 
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* EVOLUTION
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** [[Unusual Motifs in Proteins]]
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** [[Conservation, Evolutionary]]
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*** [[Cation-pi_interactions]]
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** [[Extremophiles]]
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*** [[Thermal_motion_of_peptide]]
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*IMMUNE SYSTEM
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** [[Intrinsically Disordered Protein]]
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**[[Major_Histocompatibility_Complex_Class_I]]
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* Carbohydrates
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**[[Carbohydrates]]
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**[[Carbohydrates II]]
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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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* Lipids
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**[[Lipids: structure and classification]]
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* METHODS OF STRUCTURE DETERMINATION
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* Diseases & Related Topics
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** X-ray
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** [[Alzheimer's Disease]]
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***[[X-ray_crystallography]]
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** [[Antibody]]
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****[[Asymmetric_Unit]]
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** [[Bacterial Infections]]
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****[[Biological_Unit]]
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** [[Cancer]]
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****[[Electron_density_maps]]
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** [[Coronavirus Disease 2019 (COVID-19)]]
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***SAXS
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** [[Diabetes & Hypoglycemia]]
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** NMR
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** [[Hemophilia]]
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***[[NMR_Ensembles_of_Models]]
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** [[HIV]]
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** Electron Microscopy
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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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* METHODS OF STRUCTURE & SEQUENCE ANALYSIS
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* Enzymes
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** STRUCTURAL ANALYSIS & VISUALIZATION
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** [[Hydrolases]]
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*** [[Chime]]
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** [[Isomerases]]
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*** Jmol
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** [[Ligases]]
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**** [[S347/Visualising_protein_structure|Visualising Protein Structure]] - Introduction to Jmol
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** [[Lyases]]
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**** [[FirstGlance_in_Jmol]]
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** [[Oxidoreductases]]
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*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
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** [[Transferases]]
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*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
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*** Homology Model
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* Gene Expression & Replication
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**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
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** [[DNA Replication]]
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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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** [[Nucleic Acids]]
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*** [[DRuMS]] - set of standard color schemes for macromolecular visualization
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** [[Regulation of Gene Expression]]
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** SEQUENCE ANALYSIS
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** [[RNAi]]
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*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]
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** [[Transcription & RNA Processing]]
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** [[Translation]]
 +
 
 +
* 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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