User:David Canner/Sandbox 6: Difference between revisions

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==Index of Topics Pages==
[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code.  [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure.  A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]].  And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages.  They are also never created automatically.


[[Image:New_yellow1.gif]] means that the article first became available in Proteopedia within the past four months, or that substantial new content was added within the past four months. See also [[What's New?]].
==Pages About Molecules (Not Titled with a PDB Code)==
The lists below (organized alphabetically and by category) are intended to include all pages about molecules or families of molecules that have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].
<big><big>'''See also: [[About Macromolecular Structure]]'''</big>, a list of pages not listed below.</big>
===Alphabetical Index of Topics Pages===
<!-- Start of topic pages. Please DON'T REMOVE -->
{{#tree:id=AlphaIndex|openlevels=0|
*A - C
**[[AChE inhibitors and substrates]], [[AChE inhibitors and substrates (Part II) | PartII]], [[AChE inhibitors and substrates (Part III) | PartIII]]
***[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]
**[[Acetylcholine]]
**[[Acetylcholinesterase]]
**[[Acid-beta-glucosidase]]
**[[Antibody]]
**[[A Physical Model of the β2-Adrenergic Receptor|β2-Adrenergic Receptor, A Physical Model of the]]
**[[Alpha-1-antitrypsin]][[Image:New_yellow1.gif]]
**[[Pore forming toxin, α-hemolsyin|α-hemolsyin]]
**[[Amino Acids]] with info about [[Selenocysteine]] and [[Pyrrolysine]]
**[[ACE|Angiotensin Converting Enzyme]]
**[[Annexin]]
**[[Antizyme Inhibitor]]
**[[Aquaporin]]
**[[ATP Phosphoribosyl Transferase]]
**[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
**[[Avidin]]
**[[Bacterial Intein-Like Domains (BILs)]]
**[[Believe It or Not!]]
**[[Biotin Protein Ligase]]
**[[C-di-GMP]]
**[[C-di-GMP signaling]]
**[[Calmodulin in motion]]
**[[Cellular Retinoic Acid Binding Protein|CRABP I (Cellular Retinoic Acid Binding Protein )]]
**[[Chitinases]]
**[[Cyt2Ba]]
*D - L
**[[David Canner's Favorites]]
**[[DHFR]]
**[[Dihydrofolate reductase]]
**[[Directed evolution]]
**[[DNA]]
**[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]
**[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)
**[[Dinoflagellate luciferase]]
**[[Doppel]]
**[[Dronpa]]
**[[Elastase]]
**[[Eglin]]
**[[Epitopes]]
**[[Eran Hodis's Favorites]]
**[[Eric Martz's Favorites]]
**[[Extremophiles]]
**[[Factor IX]]
**[[Fibrin]]
**[[Ferredoxin]] [[Image:New_yellow1.gif]]
**[[Filamin]]
**[[Flavodoxin]]
**[[G3p]]
**[[Gelsolin]]
**[[Glycine]]
**[[Glutamate receptor (GluA2)|The Glutamate Receptor]]
**[[Gramicidin Channel in Lipid Bilayer]] [[Image:New_yellow1.gif]]
**[[Green Fluorescent Protein]]
**Helix-turn-helix motif]]
**[[Heme]]
**[[Hemoglobin]]
**[[Pore forming toxin, α-hemolsyin|hemolsyin]]
**[[High school teachers' resources]]
**[[Highest impact structures]]
**[[Hint auto-proteolytic protein-processing domains]]
**[[HIV-1 protease]]
**[[HIV-1 Gag]]
**[[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
**[[User:Eric Martz/Molecular Playground/HIVDrug|HIV Drug]]
**[[Herpes Simplex Virus Thymidine Kinase]]
**[[HMGR|HMG-CoA Reductase]]
**[[IgA]]
**[[Influenza hemagglutinin]]
**[[Intrinsically Disordered Protein]]
**[[Ion channels]]
**[[User:Wayne Decatur/kink-turn motif|Kink-turn motif]]
**[[Kinesin-5]]
**[[Lac repressor]]
**[[Lactose Permease]]
**[[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit|Large Ribosomal Subunit]] [[Image:New_yellow1.gif]]
**[[Luciferase]]
*M - P
**[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]
**[[Matrix metalloproteinases]]
**[[Mechanosensitive channels: opening and closing]] (includes morphs)
**[[Membrane proteins]]
**[[Metal-Ligand Polyhedra]]  [[Image:New_yellow1.gif]]
**[[Metalloproteases]]
**[[Monoclonal Antibody]]
**[[Morphs]] of conformational changes of macromolecules
**[[Myoglobin]]
**[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]
**[[Nobel Prizes for 3D Molecular Structure]] including the 2009 Chemistry Prize for the [[Ribosome]]
**[[Non-Standard Residues]], see also [[Standard Residues]]
**[[Nucleoporin]]
**[[Nucleosomes]]
**[[OhrR]]
**[[P53]]
**[[PPAR|Peroxisome Proliferator-Activated Receptor]]
**[[PcrA helicase]]
**[[Personal favorites]]
**[[Phosphoglucose isomerase]]
**[[Photosystem II]]
**[[Plant Viral Protein p19 Suppression of RNA Silencing]]  [[Image:New_yellow1.gif]]
**[[Porin]]
**[[Prion protein]]
**[[Proton Channels]] (Includes an animated morph)
**[[Pyrrolysine]]
**[[Pyruvate phosphate dikinase]]
*R - Z
**[[Recombinase A]]
**[[Recoverin, a calcium-activated myristoyl switch]]
**[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]
**[[Resolvase]]
**[[Reverse transcriptase]]
**[[Ribosome]]
**[[RNA motifs]]
**[[Rop protein]]
**[[SGAP]]
**[[Scene authoring tools]]
**[[SelB Recognition]]
**[[Selenocysteine]]
**[[Serine Protease]]
**[[Serine hydrolase]]
**[[Serum Paraoxonase]]
**[[Severin]]
**[[Site | Sites, Functional]]
**[[Standard Residues]] (see also [[Non-Standard Residues]]
**[[Strictisidine Synthase]]
**[[Highest impact structures|Structures saving the most lives]]
**[[A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35|Structure of GNNQQNY from Sup35]]
**[[Suppression of RNA Silencing by Viruses]]
**[[TATA-Binding Protein]]
**[[Teaching Strategies Using Proteopedia]]
**[[Telomerase]]
**[[TEM1-beta-Lactamase/beta-lactamase Inhibitor Protein (BLIP)]]
**[[Tetrameric alcohol dehydrogenases]]
**[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]
**[[Transcription Termination Factor Rho]]
**[[Treatment of Gaucher disease]]
**[[Tropomyosin]]
**[[VEGF|Vascular Endothelial Growth Factor]]
**[[VEGFR|Vascular Endothelial Growth Factor Receptor]]
**[[Villin]]
**[[Vinculin]]
**[[VirE1/VirE2]]
**[[Z-DNA]]
**[[Zinc Fingers]]
*Well Developed PDB Code Pages
**[[1d9z]] The DNA repair protein UVRB in complex with ATP
**[[1gm5]] ''Thermotoga maritima'' RecG in complex with a synthetic three-way DNA junction resembling a stalled replication fork. [[Image:New_yellow1.gif]]
**[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.
**[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''
**[[1n4n]] Defensin from ''Petunia''
**[[1ogs]] Human acid-beta-glucosidase
**[[1v04]] Paraoxonase-1 via directed evolution
**[[1xjo]] Aminopeptidase
**[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.
**[[2db3]] ''Drosophila melanogaster''DEAD-box helicase protein Vasa. [[Image:New_yellow1.gif]]
**[[2eyq]] ''Escherichia coli'' Mfd (TRCF, transcription-repair coupling factor). [[Image:New_yellow1.gif]]
**[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family
**[[2p18]] ''Leishmania infantum'' Glyoxalase II
**[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.
**[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase
**[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family
**[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state
**[[3ews]] Human DExD/H-box RNA-dependent ATPase DDX19 in the open and [[3g0h|closed]] cleft conformation (includes morph). [[Image:New_yellow1.gif]]
**[[3dmq]] ''Escherichia coli'' Swi2/Snf2 protein RapA that recycles RNA polymerase during transcription. [[Image:New_yellow1.gif]]
**[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp
}}
===Topics Pages Organized by Category===
{{#tree:id=IndexByTopic|openlevels=0|
* Biomolecules
** [[About Macromolecular Structure]]
** Nucleotides, Nucleic Acids and Genetic Information
*** DNA
**** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]
*** RNA
**** [[RNA]]
**** RNA motifs
***** [[RNA motifs]]
***** [[User:Wayne Decatur/kink-turn motif|Kink-turn motif]]
** 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]]
*** 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]]
*** [[Luciferase]]
*** [[Dinoflagellate luciferase]]
** 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]]
***[[Glutamate receptor (GluA2)|Glutamate Receptor]]
*** [[Lactose Permease]]
*** [[Proton Channels]]
*** [[Ion Channels]]
**** [[M2 Proton Channel]]
**** [[Voltage-gated calcium channels]]
****[[Glutamate receptor (GluA2)|Glutamate Receptor]]
*** [[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
*** [[Suppression of RNA Silencing by Viruses]]
*** Filamentous bacteriophage
**** [[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]]
* 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]]
* Evolution
** [[Conservation, Evolutionary]]
** [[Extremophiles]]
* 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 %28PFK%29]]
*** [[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]]
* Fibrous Proteins
** [[Coiled coil]]
** [[Collagen]]
* 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
*** T-box family
**** [[T-box proteins]]
**** [[Brachyury]]
**** [[TBX1]]
**** [[TBX3]]
**** [[TBX5]]
**** [[TBX15]]
*** [[C-Myc]]
*** [[Lac repressor]]
*** [[Reverse transcriptase]]
*** [[TATA-Binding Protein]]
*** [[RSP1275]]
*** [[Transcription Termination Factor Rho]]
** Protein Synthesis
*** [[1fnm|Ef-G]]
*** [[Ribosome]]
*** [[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit]]
*** [[Ribosomal back translocase|ribosomal back translocase, Escherichia coli LepA]]
*** [[SelB Recognition]]
*** [[1ehz|tRNA]]
** Regulation of Gene Expression
*** [[Lac repressor]]
*** [[Irr]] (Iron Response Regulator )
*** Oncogenes
**** [[P53]]
**** [[SRC]]
*** [[Tangible Models of Cdc42 Interacting With Intersectin]]
* Immune System
** Antibodies
*** [[IgA]]
*** [[Epitopes]]
** [[Major Histocompatibility Complex Class I]]
*** [[Human beta two microglobulin]]
* Membrane Transport Proteins
** [[A Physical Model of the β2-Adrenergic Receptor]]
** [[Glutamate receptor (GluA2)|Glutamate 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]]
** [[Pore forming toxin, α-hemolsyin|The pore forming toxin, &#945;-hemolsyin]]
* Metabolism
** Introduction to Metabolism
** Glucose Catabolism
*** [[Triose Phosphate Isomerase]]
***[[Phosphofructokinase %28PFK%29]]
** 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]]
* Myoglobin & Hemoglobin
** [[Myoglobin]]
** [[Hemoglobin]]; [[Hemoglobin (Hebrew)]]
* Nervous System Proteins
** [[Acetylcholinesterase]] (AChE)
*** [[Acetylcholine]]
*** [[Flexibility of aromatic residues in acetylcholinesterase]]
** [[Acetylcholine binding protein]]  (AChBP)
** [[Butyrylcholinesterase]] (BChE)
** [[Glutamate receptor (GluA2)|Glutamate Receptor]]
* Prions and Intrinsically Disordered Proteins
** [[Prion protein]]
** [[Doppel]]
** [[Intrinsically Disordered Protein]]
* Toxins
** [[Pore forming toxin, α-hemolsyin|The pore forming toxin, &#945;-hemolsyin]]
** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
}}

Latest revision as of 04:47, 19 July 2012

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