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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. | | 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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| <big>
| | '''When you create a new page in Proteopedia, please add it to corresponding topic subpages.''' |
| {{#tree:id=siteTree|openlevels=1|close=top|open=top|
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| * Introduction to Structural Biology
| | ==Topics Pages Organized by Category== |
| ** See [[About Macromolecular Structure]]
| | {{#tree:id=OrganizedByTopic|openlevels=0| |
| ** Water
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| *** [[Water in macromolecular models|Water in Macromolecular Models]]
| | * [[Introduction to protein structure]] - A introductory overview of protein structure. |
| ** Key Chemical Concepts for Structural Biology
| | * [[About Macromolecular Structure]] - List of pages about macromolecular structure terms and concepts. |
| | | * [[Proteopedia:Topic Pages|Topic pages]] - List of pages about specific proteins or protein families. |
| *** [[Amino Acids]]
| | * [[Index pages]] - List of pages that list other pages within Proteopedia. |
| *** [[Cation-pi interactions]]
| | * Basics of Protein Structure |
| *** [[Hydrogen bond]]
| | **[[Introduction to protein structure]] - A introductory overview of protein structure |
| *** [[Hydrogen in macromolecular models|Hydrogen in Macromolecular Models]]
| | **[[Proteins: primary and secondary structure]] |
| *** [[Isoelectric point]]
| | **[[Myoglobin of Physeter catodon: structure]] |
| *** [[Salt bridges]] | | ** The Building Blocks |
| | |
| * Biomolecules
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| ** [[About Macromolecular Structure]]
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| ** Nucleotides, Nucleic Acids and Genetic Information
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| *** DNA
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| **** [[DNA]]
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| **** B-DNA [[1bna]] | |
| **** [[Z-DNA]]
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| | |
| ** Amino Acids | |
| *** [[Amino Acids]] | | *** [[Amino Acids]] |
| *** [[Selenocysteine]] | | *** [[Backbone_representations]] |
| ** Proteins, Primary Structure
| | *** [[Peptide]] |
| *** [[Conservation, Evolutionary]]
| | **** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]] |
| *** [[Isoelectric point]] | | **** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]] |
| | |
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| ** Proteins, Three-Dimensional Structure | |
| *** [[User:Tommie_Hata/Protein_Structure_Tutorial]] | |
| *** [[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]] | |
| *** 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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| **** [[A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35]]
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| ** Colored Proteins & those that Change Color | | ** Conformational flexibility of a polypeptide chain |
| *** [[Green Fluorescent Protein]]; [[GFP (Hebrew)]] | | *** [[Phi and Psi Angles]] |
| *** [[Dronpa]] | | *** [[Ramachandran Plots]] |
| *** [[Factor IX]] | | *** [[Tutorial:Ramachandran principle and phi psi angles]] |
| | ** [[Secondary structure]] |
| | *** [[Helices in Proteins]] |
| | **** [[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]] |
| | *** [[Sheets in Proteins]] |
| | **** [[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]] |
| | ** [[Structural_templates]] |
| | *** [[Globular_Proteins]] |
| | **** [[Turns in Proteins]] |
| | *** [[Fibrous Proteins]] |
| | **** [[Coiled_coil]] |
| | **** [[Collagen]] - Illustrates the structure of a collagen segment as well as the structure of a mutated tropocollagen. |
| | **** [[Fibroins]] |
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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
| | ** [[Unusual Motifs in Proteins]] |
| *** Antibodies
| | *** [[Cation-pi_interactions]] |
| **** [[IgA]]
| | *** [[Thermal_motion_of_peptide]] |
| **** [[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]] | |
| **** [[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
| | ** [[Intrinsically Disordered Protein]] |
| *** [[Prion protein]]
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| *** [[Doppel]]
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| *** [[Intrinsically Disordered Protein]]
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| ** Toxins | | * Carbohydrates |
| *** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]] | | **[[Carbohydrates]] |
| | **[[Carbohydrates II]] |
| | * Cytoskeletal Proteins |
| | ** [[Actin]] |
| | ** [[Keratins]] |
| | ** [[Tropomyosin]] |
| | ** [[Tubulin]] |
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| ** Mitosis, Meiosis and Cargo Transport Proteins | | * Lipids |
| *** [[Kinesin-5]]
| | **[[Lipids: structure and classification]] |
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| ** Viruses | | * Diseases & Related Topics |
| *** [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
| | ** [[Alzheimer's Disease]] |
| *** Filamentous bacteriphage | | ** [[Antibody]] |
| **** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage | | ** [[Bacterial Infections]] |
| *** HIV | | ** [[Cancer]] |
| **** [[HIV-1 protease]] | | ** [[Coronavirus Disease 2019 (COVID-19)]] |
| **** [[HIV-1 Gag]]
| | ** [[Diabetes & Hypoglycemia]] |
| **** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]] | | ** [[Hemophilia]] |
| **** [[User:Eric Martz/Molecular Playground/HIVDrug]] | | ** [[HIV]] |
| *** Herpes Simplex Virus | | ** [[Hypertension & Congestive Heart Failure]] |
| **** [[Herpes Simplex Virus Thymidine Kinase]] | | ** [[Immune Response]] |
| *** Influenza | | ** [[Inflammation & Rheumatoid Arthritis]] |
| **** [[Influenza hemagglutinin]] | | ** [[Influenza]] |
| **** [[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
| | ** [[Metabolic Disorders]] |
| | ** [[Neurodevelopmental Disorders]] |
| | ** [[Oncogenes]] |
| | ** [[Pharmaceutical Drugs]] |
| | ** [[Pharmaceutical Drug Targets]] |
| | ** [[Toxins]] |
| | ** [[Viral Infections]] |
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| * Enzymes | | * Enzymes |
| ** Enzymatic Catalysis | | ** [[Hydrolases]] |
| *** Acid-beta-glucosidase | | ** [[Isomerases]] |
| **** reHuman Acid-beta-glucosidase made in CHO cells [[1ogs]]
| | ** [[Ligases]] |
| **** reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide [[1y7v]] | | ** [[Lyases]] |
| **** reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin [[2v3d]] | | ** [[Oxidoreductases]] |
| **** Velaglucerase Alfa [[2wkl]] | | ** [[Transferases]] |
| *** Acid Proteases
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| **** [[HIV-1 protease]]
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| **** [[Streptomyces griseus Aminopeptidase (SGAP)]]; [[Aminopeptidase]] | | * Gene Expression & Replication |
| *** [[Aconitase]]
| | ** [[DNA Replication]] |
| *** Cysteine Proteases
| | ** [[Nucleic Acids]] |
| *** [[Hen Egg-White (HEW) Lysozyme]]
| | ** [[Regulation of Gene Expression]] |
| *** [[Choline Oxidase]]
| | ** [[RNAi]] |
| *** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
| | ** [[Transcription & RNA Processing]] |
| *** [[Metalloproteases]]
| | ** [[Translation]] |
| **** [[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]], [[NOS structures]]
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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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| *** [[C-di-GMP signaling]]
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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 |
| | ** [[Group:MUZIC|Muscle sarcomere: Z-Disk]] |
| | ** [[Ribosome]] |
| | ** [[Ribosoma 70S]] |
| | ** [[Nucleosomes]] |
| | ** [[Nucleosome structure]] |
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| * Metabolism | | * Metabolism |
| ** Introduction to Metabolism | | ** [[Amino Acid Synthesis & Metabolism]] |
| | ** [[Carbohydrate Metabolism]] |
| | ** [[Photosynthesis]] |
| | ** [[Regulation of Gene Expression]] |
| | ** [[Drug Metabolism by CYP450 Enzymes]] |
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| ** Glucose Catabolism | | * Miscellaneous |
| *** [[Triose Phosphate Isomerase]]
| | ** [[Colored & Bioluminescent Proteins]] |
| ***[[Phosphofructokinase %28PFK%29]]
| | ** [[Coronavirus Disease 2019 (COVID-19)]] |
| | | ** [[Enzimas: complejo enzima-sustrato]] |
| | | ** [[3D Molecular Models]] |
| ** 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 | | * Signaling & Transport |
| *** [[Aconitase]]
| | ** [[Hormone]] |
| | ** [[Membrane Channels & Pumps]] |
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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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|
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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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|
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| * Gene Expression and Replication
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|
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|
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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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|
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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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|
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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]] (Iron Response Regulator )
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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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|
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| * Evolution
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| ** [[Conservation, Evolutionary]]
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|
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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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|
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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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|
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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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|
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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
| |
| **** [[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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|
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| ** Sequence Analysis
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| *** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]
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|
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| * Model Structures
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| ** See [[Theoretical models]]
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| ** [[African Malaria Mosquito Acetylcholinesterase]]
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| ** [[Structure of E. coli DnaC helicase loader]]
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| ** [[User:Yuan-Ping Pang/HAB•BoNTAe]]
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|
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| * Miscellaneous
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| ** [[Molecular Playground]]
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| ** [[Research Groups]]
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| }} | | }} |
| </big>
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