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| ==Index of Topics Pages==
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| [[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.
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| [[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?]].
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| ==Pages About Molecules (Not Titled with a PDB Code)==
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|
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| The lists below (organized alphabetically and by category) are intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also 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 Because this list is manually maintained, it may be out of date.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]].
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| <big><big>'''See also: [[About Macromolecular Structure]]'''</big>, a list of pages not listed below.</big>
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| ===Alphabetical Index of Topics Pages===
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| <!-- Start of topic pages. Please DON'T REMOVE -->
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| {{#tree:id=AlphaIndex|openlevels=0|
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| *A - C
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| **[[AChE inhibitors and substrates]], [[AChE inhibitors and substrates (Part II) | PartII]], [[AChE inhibitors and substrates (Part III) | PartIII]]
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| ***[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]
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| **[[Acetylcholine]]
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| **[[Acetylcholinesterase]]
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| **[[Acid-beta-glucosidase]]
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| **[[Antibody]]
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| **[[A Physical Model of the β2-Adrenergic Receptor|β2-Adrenergic Receptor, A Physical Model of the]]
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| **[[Alpha-1-antitrypsin]][[Image:New_yellow1.gif]]
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| **[[Pore forming toxin, α-hemolsyin|α-hemolsyin]]
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| **[[Amino Acids]] with info about [[Selenocysteine]] and [[Pyrrolysine]]
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| **[[Annexin]]
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| **[[Antizyme Inhibitor]]
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| **[[Aquaporin]]
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| **[[ATP Phosphoribosyl Transferase]]
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| **[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
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| **[[Avidin]]
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| **[[Bacterial Intein-Like Domains (BILs)]]
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| **[[Believe It or Not!]]
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| **[[Biotin Protein Ligase]]
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| **[[C-di-GMP]]
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| **[[C-di-GMP signaling]]
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| **[[Chitinases]]
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| **[[Cyt2Ba]]
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|
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| *D - L
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| **[[DHFR]]
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| **[[Dihydrofolate reductase]]
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| **[[Directed evolution]]
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| **[[DNA]]
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| **[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]
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| **[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)
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| **[[Dinoflagellate luciferase]]
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| **[[Doppel]]
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| **[[Dronpa]]
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| **[[Elastase]]
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| **[[Eglin]]
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| **[[Eran Hodis's Favorites]]
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| **[[Eric Martz's Favorites]]
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| **[[Extremophiles]]
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| **[[Fibrin]]
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| **[[Ferredoxin]] [[Image:New_yellow1.gif]]
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| **[[Filamin]]
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| **[[Flavodoxin]]
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| **[[Gelsolin]]
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| **[[Glycine]]
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| **[[Glutamate receptor (GluA2)|The Glutamate Receptor]]
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| **[[Gramicidin Channel in Lipid Bilayer]] [[Image:New_yellow1.gif]]
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| **[[Green Fluorescent Protein]]
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| **[[Heme]]
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| **[[Hemoglobin]]
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| **[[Pore forming toxin, α-hemolsyin|hemolsyin]]
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| **[[High school teachers' resources]]
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| **[[Highest impact structures]]
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| **[[Hint auto-proteolytic protein-processing domains]]
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| **[[Intrinsically Disordered Protein]]
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| **[[Ion channels]]
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| **[[Lac repressor]]
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| **[[Lactose Permease]]
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| **[[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit|Large Ribosomal Subunit]] [[Image:New_yellow1.gif]]
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| **[[Luciferase]]
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|
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| *M - P
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| **[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]
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| **[[Matrix metalloproteinases]]
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| **[[Mechanosensitive channels: opening and closing]] (includes morphs)
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| **[[Membrane proteins]]
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| **[[Metal-Ligand Polyhedra]] [[Image:New_yellow1.gif]]
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| **[[Metalloproteases]]
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| **[[Morphs]] of conformational changes of macromolecules
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| **[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]
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| **[[Nobel Prizes for 3D Molecular Structure]] including the 2009 Chemistry Prize for the [[Ribosome]]
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| **[[Non-Standard Residues]], see also [[Standard Residues]]
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| **[[Nucleoporin]]
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| **[[Nucleosomes]]
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| **[[OhrR]]
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| **[[P53]]
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| **[[PcrA helicase]]
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| **[[Personal favorites]]
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| **[[Phosphoglucose isomerase]]
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| **[[Photosystem II]]
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| **[[Plant Viral Protein p19 Suppression of RNA Silencing]] [[Image:New_yellow1.gif]]
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| **[[Porin]]
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| **[[Prion protein]]
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| **[[Proton Channels]] (Includes an animated morph)
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| **[[Pyrrolysine]]
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| **[[Pyruvate phosphate dikinase]]
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|
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| *R - Z
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| **[[Recombinase A]]
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| **[[Recoverin, a calcium-activated myristoyl switch]]
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| **[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]
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| **[[Resolvase]]
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| **[[Reverse transcriptase]]
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| **[[Ribosome]]
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| **[[RNA motifs]]
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| **[[Rop protein]]
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| **[[SGAP]]
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| **[[Scene authoring tools]]
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| **[[SelB Recognition]]
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| **[[Selenocysteine]]
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| **[[Serine Protease]]
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| **[[Serine hydrolase]]
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| **[[Serum Paraoxonase]]
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| **[[Severin]]
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| **[[Site | Sites, Functional]]
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| **[[Standard Residues]] (see also [[Non-Standard Residues]]
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| **[[Strictisidine Synthase]]
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| **[[Highest impact structures|Structures saving the most lives]]
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| **[[Suppression of RNA Silencing by Viruses]]
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| **[[TATA-Binding Protein]]
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| **[[Teaching Strategies Using Proteopedia]]
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| **[[Telomerase]]
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| **[[TEM1-beta-Lactamase/beta-lactamase Inhibitor Protein (BLIP)]]
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| **[[Tetrameric alcohol dehydrogenases]]
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| **[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]
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| **[[Transcription Termination Factor Rho]]
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| **[[Treatment of Gaucher disease]]
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| **[[Tropomyosin]]
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| **[[Villin]]
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| **[[Vinculin]]
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| **[[VirE1/VirE2]]
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| **[[Zinc Fingers]]
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| *Well Developed PDB Code Pages
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| Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.
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|
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| **[[1d9z]] The DNA repair protein UVRB in complex with ATP
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| **[[1gm5]] ''Thermotoga maritima'' RecG in complex with a synthetic three-way DNA junction resembling a stalled replication fork. [[Image:New_yellow1.gif]]
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| **[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.
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| **[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''
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| **[[1n4n]] Defensin from ''Petunia''
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| **[[1ogs]] Human acid-beta-glucosidase
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| **[[1v04]] Paraoxonase-1 via directed evolution
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| **[[1xjo]] Aminopeptidase
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| **[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.
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| **[[2db3]] ''Drosophila melanogaster''DEAD-box helicase protein Vasa. [[Image:New_yellow1.gif]]
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| **[[2eyq]] ''Escherichia coli'' Mfd (TRCF, transcription-repair coupling factor). [[Image:New_yellow1.gif]]
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| **[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family
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| **[[2p18]] ''Leishmania infantum'' Glyoxalase II
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| **[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.
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| **[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase
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| **[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family
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| **[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state
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| **[[3ews]] Human DExD/H-box RNA-dependent ATPase DDX19 in the open and [[3g0h|closed]] cleft conformation (includes morph). [[Image:New_yellow1.gif]]
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| **[[3dmq]] ''Escherichia coli'' Swi2/Snf2 protein RapA that recycles RNA polymerase during transcription. [[Image:New_yellow1.gif]]
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| **[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp
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| }}
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|
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| ===Topics Pages Organized by Category===
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| {{#tree:id=IndexByTopic|openlevels=0|
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|
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| * Biomolecules
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| ** [[About Macromolecular Structure]]
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|
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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]]
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| **** [[Z-DNA]]
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| *** RNA
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| **** [[RNA]]
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| **** RNA motifs
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| ***** [[RNA motifs]]
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| ***** [[User:Wayne Decatur/kink-turn motif|Kink-turn motif]]
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|
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| ** Proteins, Three-Dimensional Structure
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| *** [[User:Tommie_Hata/Protein_Structure_Tutorial]]
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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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|
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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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|
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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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| *** [[Luciferase]]
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| *** [[Dinoflagellate luciferase]]
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|
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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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|
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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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| ** 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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| ***[[Glutamate receptor (GluA2)|Glutamate Receptor]]
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| *** [[Lactose Permease]]
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| *** [[Proton Channels]]
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| *** [[Ion Channels]]
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| **** [[M2 Proton Channel]]
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| **** [[Voltage-gated calcium channels]]
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| ****[[Glutamate receptor (GluA2)|Glutamate Receptor]]
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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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|
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| ** Prions and Intrinsically Disordered Proteins
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| *** [[Prion protein]]
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| *** [[Doppel]]
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| *** [[Intrinsically Disordered Protein]]
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|
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| ** Toxins
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| *** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
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|
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| ** Mitosis, Meiosis and Cargo Transport Proteins
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| *** [[Kinesin-5]]
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|
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| ** Viruses
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| *** [[Suppression of RNA Silencing by Viruses]]
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| *** Filamentous bacteriophage
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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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| **** [[User:Eric Martz/Molecular Playground/HIVDrug]]
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| *** Herpes Simplex Virus
| |
| **** [[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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|
| |
| * 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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|
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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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| * Evolution
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| ** [[Conservation, Evolutionary]]
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| ** [[Extremophiles]]
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|
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| * Enzymes
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| ** Enzymatic Catalysis
| |
| *** Acid-beta-glucosidase
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| **** reHuman Acid-beta-glucosidase made in CHO cells [[1ogs]]
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| **** reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide [[1y7v]]
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| **** reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin [[2v3d]]
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| **** Velaglucerase Alfa [[2wkl]]
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| *** Acid Proteases
| |
| **** [[HIV-1 protease]]
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|
| |
| **** [[Streptomyces griseus Aminopeptidase (SGAP)]]; [[Aminopeptidase]]
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| *** [[Aconitase]]
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| *** Cysteine Proteases
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| *** [[Hen Egg-White (HEW) Lysozyme]]
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| *** [[Choline Oxidase]]
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| *** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
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| *** [[Metalloproteases]]
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| **** [[Matrix metalloproteinases]]
| |
| *** 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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|
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| ** Enzymes - Molecular Machines
| |
| *** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
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| *** [[Pyruvate phosphate dikinase]]
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|
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| * Fibrous Proteins
| |
| ** [[Coiled coil]]
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| ** [[Collagen]]
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|
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|
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| * Gene Expression and Replication
| |
| ** Nucleic Acid Structure
| |
| *** [[DNA]]
| |
| **** 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
| |
| *** [[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]]
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| *** [[Rop protein]]
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|
| |
| ** 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, α-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, α-hemolsyin]]
| |
| ** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
| |
| }}
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