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
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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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==Topics Pages Organized by Category==
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*** [[Water_in_macromolecular_models|Water in Macromolecular Models]]
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* [[Introduction to protein structure]] - A introductory overview of protein structure.
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** Key Chemical Concepts for Structural Biology
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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
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*** [[Amino Acids]]
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*** [[Backbone_representations]]
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*** [[Peptide]]
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**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
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**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
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*** [[Amino_Acids]]
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** Conformational flexibility of a polypeptide chain
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*** [[Cation-pi interactions]]
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*** [[Phi and Psi Angles]]
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*** [[Hydrogen bond]]
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*** [[Ramachandran Plots]]
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*** [[Hydrogen_in_macromolecular_models|Hydrogen in Macromolecular Models]]
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*** [[Tutorial:Ramachandran principle and phi psi angles]]
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*** [[Isoelectric_point]]
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** [[Secondary structure]]
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*** [[Helices in Proteins]]
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* Biomolecules
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**** [[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
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** [[About_Macromolecular_Structure]]
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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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** Nucleotides, Nucleic Acids and Genetic Information
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** [[Structural_templates]]
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*** DNA
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*** [[Globular_Proteins]]
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**** [[DNA]]
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**** [[Turns in Proteins]]
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**** B-DNA [[1bna]]
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*** [[Fibrous Proteins]]
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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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*** [[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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* 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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** Membrane Transport Proteins
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* Lipids
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*** [[A Physical Model of the β2-Adrenergic Receptor]]
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**[[Lipids: structure and classification]]
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*** [[Lactose_Permease]]
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*** [[Proton_Channels]]
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*** [[Ion_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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* Diseases & Related Topics
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*** [[Prion_protein]]
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** [[Alzheimer's Disease]]
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*** [[Doppel]]
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** [[Antibody]]
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*** [[Intrinsically Disordered Protein]]
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** [[Bacterial Infections]]
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** [[Cancer]]
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** Toxins
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** [[Coronavirus Disease 2019 (COVID-19)]]
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*** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
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** [[Diabetes & Hypoglycemia]]
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** [[Hemophilia]]
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** Mitosis, Meiosis and Cargo Transport Proteins
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** [[HIV]]
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*** [[Kinesin-5]]
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** [[Hypertension & Congestive Heart Failure]]
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** [[Immune Response]]
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** Viruses
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** [[Inflammation & Rheumatoid Arthritis]]
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*** [[User:Wayne_Decatur/Suppression_of_RNA_Silencing_by_Viruses]]
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** [[Influenza]]
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*** Filamentous bacteriphage
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** [[Metabolic Disorders]]
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**** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage
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** [[Neurodevelopmental Disorders]]
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*** HIV
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** [[Oncogenes]]
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**** [[HIV-1 protease]]
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** [[Pharmaceutical Drugs]]
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**** [[HIV-1 Gag]]
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** [[Pharmaceutical Drug Targets]]
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**** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
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** [[Toxins]]
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**** [[User:Eric_Martz/Molecular_Playground/HIVDrug]]
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** [[Viral Infections]]
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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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**** [[Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza]]
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* Enzymes
* Enzymes
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** Enzymatic Catalysis
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** [[Hydrolases]]
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***[[Hen_Egg-White_%28HEW%29_Lysozyme]]
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** [[Isomerases]]
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*** Serine Hydrolases
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** [[Ligases]]
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**** [[Serine_Protease]]
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** [[Lyases]]
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**** [[Trypsin]]
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** [[Oxidoreductases]]
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**** [[Alpha-1-antitrypsin]]
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** [[Transferases]]
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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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*** Cysteine Proteases
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**** [[Tobacco_Etch_Virus_(TEV)_Protease]]
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**** [[Streptomyces_griseus_Aminopeptidase_(SGAP)]]; [[Aminopeptidase]]
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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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*** [[Triose_Phosphate_Isomerase]]
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*** [[Aconitase]]
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*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
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*** [[Pyruvate_phosphate_dikinase]]
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***[[Phosphofructokinase_%28PFK%29]]
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** Enzyme Kinetics, Inhibition, and Control
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* Gene Expression & Replication
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***[[Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza]]
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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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** Biochemical Signaling
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* Large Macromolecular Assemblies
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*** [[Nitric_oxide_synthase]]
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** [[Group:MUZIC|Muscle sarcomere: Z-Disk]]
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*** [[Recoverin,_a_calcium-activated_myristoyl_switch]]
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** [[Ribosome]]
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*** [[Bcl-2]]
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** [[Ribosoma 70S]]
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*** [[C-Myc]]
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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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** Glucose Catabolism
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** [[Photosynthesis]]
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*** [[Triose_Phosphate_Isomerase]]
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** [[Regulation of Gene Expression]]
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***[[Phosphofructokinase_%28PFK%29]]
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** [[Drug Metabolism by CYP450 Enzymes]]
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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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*** [[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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*** [[P53]]
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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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* 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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* Miscellaneous
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** Structural Analysis & Visualization
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** [[Colored & Bioluminescent Proteins]]
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*** [[Chime]]
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** [[Coronavirus Disease 2019 (COVID-19)]]
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*** Jmol
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** [[Enzimas: complejo enzima-sustrato]]
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**** [[S347/Visualising_protein_structure|Visualising Protein Structure]] - Introduction to Jmol
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** [[3D Molecular Models]]
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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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* Signaling & Transport
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*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]
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** [[Hormone]]
 +
** [[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



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