Proteopedia:Table of Contents

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.

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• Introduction to Structural Biology
  • See About Macromolecular Structure
  • Water
    • Water in Macromolecular Models
  • Key Chemical Concepts for Structural Biology
    • Amino Acids
    • Cation-pi interactions
    • Hydrogen bond
    • Hydrogen in Macromolecular Models
    • Isoelectric point
    • Salt bridges
• Biomolecules
  • About Macromolecular Structure
  • Nucleotides, Nucleic Acids and Genetic Information
    • DNA
      • DNA
      • B-DNA 1bna
      • Z-DNA
  • Amino Acids
    • Amino Acids
    • Selenocysteine
  • Proteins, Primary Structure
    • Conservation, Evolutionary
    • Isoelectric point
  • Proteins, Three-Dimensional Structure
    • User:Tommie_Hata/Protein_Structure_Tutorial
    • S347/The four tiers of protein structure
    • Secondary structure
    • Protein structural motifs
      • User:James D Watson/Structural Templates
    • Fibrous Proteins
      • Coiled coil
      • Collagen
    • Protein Misfolding
      • Prion protein
      • A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35
  • Colored Proteins & those that Change Color
    • Green Fluorescent Protein; GFP (Hebrew)
    • Dronpa
    • Factor IX
  • DNA Binding Proteins
    • Helix-turn-helix motif
    • DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1
  • Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
    • Antibodies
      • IgA
      • Epitopes
      • Major Histocompatibility Complex Class I
    • Calmodulin in motion
    • Myoglobin
    • Hemoglobin; Hemoglobin (Hebrew)
    • Kinesin-5
  • Lipids and Biological Membranes
  • Lipid Binding Proteins
    • CRABP I ( Cellular Retinoic Acid Binding Protein )
  • Membrane Transport Proteins
    • A Physical Model of the β2-Adrenergic Receptor
    • Lactose Permease
    • Proton Channels
    • Ion channels
      • M2 Proton Channel
      • Voltage-gated calcium channels
    • Mechanosensitive channels: opening and closing
    • Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
  • Prions and Intrinsically Disordered Proteins
    • Prion protein
    • Doppel
    • Intrinsically Disordered Protein
  • Toxins
    • Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis
  • Mitosis, Meiosis and Cargo Transport Proteins
    • Kinesin-5
  • Viruses
    • User:Wayne Decatur/Suppression of RNA Silencing by Viruses
    • Filamentous bacteriphage
      • G3p - minor coat protein found on the surface of filamentous bacteriophage
    • HIV
      • HIV-1 protease
      • HIV-1 Gag
      • HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process
      • User:Eric Martz/Molecular Playground/HIVDrug
    • Herpes Simplex Virus
      • Herpes Simplex Virus Thymidine Kinase
    • Influenza
      • Influenza hemagglutinin
      • Avian Influenza Neuraminidase, Tamiflu and Relenza
• Enzymes
  • Enzymatic Catalysis
    • Acid-beta-glucosidase
      • reHuman Acid-beta-glucosidase made in CHO cells 1ogs
      • reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide 1y7v
      • reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin 2v3d
      • Velaglucerase Alfa 2wkl
    • Acid Proteases
      • HIV-1 protease
      • Streptomyces griseus Aminopeptidase (SGAP); Aminopeptidase
    • Aconitase
    • Cysteine Proteases
    • Hen Egg-White (HEW) Lysozyme
    • Choline Oxidase
    • Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
    • Metalloproteases
      • Matrix metalloproteinases
    • Oxidoreductases
      • NADH quinone oxidoreductase
    • Phosphofructokinase (PFK)
    • Pyruvate phosphate dikinase
    • Serotonin N-acetyltransferase
    • Serine Hydrolases
      • Acetylcholinesterase (AChE)
        • Acetylcholine
        • Flexibility of aromatic residues in acetylcholinesterase
        • AChE inhibitors and substrates
          • 1eve AChE-Aricept complex; 1eve (Arabic); 1eve (Chinese); 1eve (Italian); 1eve (Russian); 1eve (Spanish); 1eve (Turkish)
          • AChE bivalent inhibitors
      • Tobacco Etch Virus (TEV) Protease
    • Serine Protease
      • Trypsin
    • Triose Phosphate Isomerase
  • Enzyme Inhibitors
    • Alpha-1-antitrypsin
  • Enzyme Kinetics, Inhibition, and Control
    • Avian Influenza Neuraminidase, Tamiflu and Relenza
  • Biochemical Signaling
    • Nitric oxide synthase, NOS structures
    • Recoverin, a calcium-activated myristoyl switch
    • Bcl-2
    • C-Myc
    • C-di-GMP signaling
  • Enzymes - Molecular Machines
    • Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
    • Pyruvate phosphate dikinase
• Metabolism
  • Introduction to Metabolism
  • Glucose Catabolism
    • Triose Phosphate Isomerase
    • Phosphofructokinase (PFK)
  • Glycogen Metabolism and Gluconeogenesis
    • Phosphoglucose isomerase
    • Calmodulin in motion
    • Biotin Protein Ligase
  • Citric Acid Cycle
    • Aconitase
  • Electron Transport and Oxidative Phosphorylation
    • NADH quinone oxidoreductase
  • Photosynthesis
    • Photosystem II
    • Ribulose-1,5-bisphosphate carboxylase/oxygenase
    • PrrA in Rhodobacter sphaeroides
    • Pyruvate phosphate dikinase
  • Lipid Metabolism
    • Acid-beta-glucosidase
  • Amino Acid Metabolism
    • Aromatic amino acid hydroxylases
    • Phenylalanine hydroxylase
    • Tyrosine hydroxylase
    • ATP Phosphoribosyl Transferase
    • Isochorismate pyruvate lyase
  • Mammalian Fuel Metabolism: Integration and Regulation
  • Nucleotide Metabolism
    • Dihydrofolate reductase
• Gene Expression and Replication
  • Nucleic Acid Structure
    • DNA
      • B-DNA 1bna
      • Z-DNA
    • Nucleosomes
  • DNA Replication, Repair, and Recombination
    • DNA Replication,Transcription and Translation
    • DNA Polymerase I
    • PcrA helicase
    • Fpg Nei Protein Superfamily - DNA Repair and Base Excision DNA Repair
    • Human RecQ-Like protein 1 - RecQ family of DNA helicases are conserved in from bacteria to man
    • Structure of E. coli DnaC helicase loader
    • 1x9n#Crystal Structure of Human DNA Ligase I bound to 5.27-adenylated.2C nicked DNA
    • Rop protein
  • Transcription and RNA Processing
    • C-Myc
    • Lac repressor
    • Reverse transcriptase
    • TATA-Binding Protein
    • RSP1275
    • Transcription Termination Factor Rho
  • Protein Synthesis
    • Ribosome
    • SelB Recognition
  • Regulation of Gene Expression
    • Lac repressor
    • Irr (Iron Response Regulator )
    • Oncogenes
      • P53
      • SRC
    • Tangible Models of Cdc42 Interacting With Intersectin
• Evolution
  • Conservation, Evolutionary
  • Extremophiles
• Immune System
  • Antibodies
    • IgA
    • Epitopes
  • Major Histocompatibility Complex Class I
    • Human beta two microglobulin
• Diseases
  • Cancer
    • SRC
    • Proteins involved in cancer
• Methods of Structure Determination
  • X-ray
    • X-ray crystallography
      • Asymmetric Unit
      • Biological Unit
      • Electron density maps
    • SAXS
  • NMR
    • NMR Ensembles of Models
  • Electron Microscopy
• Methods of Structure & Sequence Analysis
  • Structural Analysis & Visualization
    • CPK - Corey-Pauling-Koltun spacefilling molecular models and color scheme for elements
    • Chime
    • Jmol
      • Visualising Protein Structure - Introduction to Jmol
      • FirstGlance in Jmol
    • Teaching Proteopedia
    • Generate Unfolded Structures
    • Homology Model
      • Homology Modeling
      • TRIM5a Homology Models - Differences in models as a function of their templates
    • DRuMS - set of standard color schemes for macromolecular visualization
  • Sequence Analysis
    • Sequence Analysis Tools
• Model Structures
  • See Theoretical models
  • African Malaria Mosquito Acetylcholinesterase
  • Structure of E. coli DnaC helicase loader
  • Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB
• Miscellaneous
  • Molecular Playground
  • Research Groups

Proteopedia Page Contributors and Editors (what is this?)

Joel L. Sussman, Judy Voet, Alexander Berchansky, Eran Hodis, Jaime Prilusky, Wayne Decatur, Eric Martz, Alejandro Porto, Angel Herraez, Karen L. Lee, Helen Ginn, Karl Oberholser, Israel Hanukoglu, Arthur Cox, Yuan-Ping Pang, Tilman Schirmer, Tomas Klumpler, David Canner