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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)


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.
'''When you create a new page in Proteopedia, please add it to corresponding topic subpages.'''


'''If you create a new page in Proteopedia, please add it to both the "Index by Topic" and the "Alphabetical Index". Also, if you find a page missing from these indices, please add it to both.'''
==Topics Pages Organized by Category==
 
{{#tree:id=OrganizedByTopic|openlevels=0|
==Index by Topic==
 
<big>
{{#tree:id=IndexByTopic|openlevels=1|close=top|open=top|
 
* Introduction to Structural Biology
** See [[About Macromolecular Structure]]
** Water
 
*** [[Water in macromolecular models|Water in Macromolecular Models]]
** Key Chemical Concepts for Structural Biology


* [[Introduction to protein structure]] - A introductory overview of protein structure.
* [[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.
* [[Index pages]] - List of pages that list other pages within Proteopedia.
* Basics of Protein Structure
**[[Introduction to protein structure]] - A introductory overview of protein structure
**[[Proteins: primary and secondary structure]]
**[[Myoglobin of Physeter catodon: structure]]
** The Building Blocks
*** [[Amino Acids]]
*** [[Amino Acids]]
*** [[Cation-pi interactions]]
*** [[Backbone_representations]]
*** [[Hydrogen bond]]
*** [[Peptide]]
*** [[Hydrogen in macromolecular models|Hydrogen in Macromolecular Models]]
**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
*** [[Isoelectric point]]
**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
*** [[Salt bridges]]


* Biomolecules
** Conformational flexibility of a polypeptide chain
** [[About Macromolecular Structure]]
*** [[Phi and Psi Angles]]
*** [[Ramachandran Plots]]
*** [[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]]


** 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]]


** [[Unusual Motifs in Proteins]]
*** [[Cation-pi_interactions]]
*** [[Thermal_motion_of_peptide]]


** Amino Acids
** [[Intrinsically Disordered Protein]]
*** [[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]]
 
*** 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
* Carbohydrates
** [[Green Fluorescent Protein]]; [[GFP (Hebrew)]]
**[[Carbohydrates]]
** [[Dronpa]]
**[[Carbohydrates II]]
** [[Factor IX]]
* Cytoskeletal Proteins
** [[Actin]]
** [[Keratins]]
** [[Tropomyosin]]
** [[Tubulin]]


* Lipids
**[[Lipids: structure and classification]]


* DNA Binding Proteins
* Diseases & Related Topics
** [[Helix-turn-helix motif]]
** [[Alzheimer's Disease]]
** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]
** [[Antibody]]
** [[Bacterial Infections]]
** [[Cancer]]
** [[Coronavirus Disease 2019 (COVID-19)]]
** [[Diabetes & Hypoglycemia]]
** [[Hemophilia]]
** [[HIV]]
** [[Hypertension & Congestive Heart Failure]]
** [[Immune Response]]
** [[Inflammation & Rheumatoid Arthritis]]
** [[Influenza]]
** [[Metabolic Disorders]]
** [[Neurodevelopmental Disorders]]
** [[Oncogenes]]
** [[Pharmaceutical Drugs]]
** [[Pharmaceutical Drug Targets]]
** [[Toxins]]
** [[Viral Infections]]


* 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
**** [[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]]
 
* 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]]
 
 
* Myoglobin & Hemoglobin
** [[Myoglobin]]
** [[Hemoglobin]]; [[Hemoglobin (Hebrew)]]
 
* Nervous System Proteins
 
** [[Acetylcholinesterase]] (AChE)
*** [[Acetylcholine]]
*** [[Flexibility of aromatic residues in acetylcholinesterase]]
 
*** AChE inhibitors (In Different Languages)
**** [[1eve]] AChE-Aricept complex, [[1eve (Arabic)]], [[1eve (Chinese)]], [[1eve (Italian)]], [[1eve (Russian)]], [[1eve (Spanish)]], [[1eve (Turkish)]]
**** [[1vot]] AChE-Huperzine A complex, [[1vot (Chinese)]]
 
 
*** Acetylcholinesterase - AChE native
**** [[3lii]] – hAChE - recombinant human
**** [[1ea5]], [[2ace]] – ''Tc''AChE – trigonal – ''Torpedo californica''
**** [[2j3d]] – ''Tc''AChE – monoclinic
**** [[1w75]] – ''Tc''AChE – orthorhombic
**** [[1eea]] – ''Tc''AChE – cubic
**** [[2vt6]], [[2vt7]] – ''Tc''AChE – different dosage
**** [[1qid]] to [[1qim]]  - ''Tc''AChE synchrotron radiation damage
**** [[1j06]], [[1maa]] – mAChE - mouse
**** [[1qo9]] – ''Dm''AChE - ''Drosophila''
**** [[1c2o]], [[1c2b]] – electrophorus AChE – Electric eel
 
*** AChE active site inhibitors conjugating at the bottom of the active site gorge
**** [[2w9i]] – ''Tc''AChE + methylene blue
**** [[2wls]] – MosAChE + AMTS13
**** [[2vq6]] – ''Tc''AChE + 2-PAM
**** [[2j3q]] – ''Tc''AChE + Thioflavin T
**** [[2ha0]] – mAChE + ketoamyltrimethylammonium
**** [[2h9y]] – mAChE + TMTFA
**** [[1gpk]], [[1gpn]], [[1vot]] – ''Tc''AChE + huperzine
**** [[1gqr]] – ''Tc''AChE + rivastigmine
**** [[1gqs]] – ''Tc''AChE + NAP
**** [[1e66]] – ''Tc''AChE + huprine
**** [[1dx4]], [[1qon]] – ''Dm''AChE + tacrine derivative
**** [[1oce]] – ''Tc''AChE + MF268
**** [[1ax9]], [[1ack]] – ''Tc''AChE + edrophonium 
**** [[1amn]] – ''Tc''AChE + TMTFA
**** [[1acj]] – ''Tc''AChE + tacrine
 
*** AChE peripheral site inhibitors conjugating at the surface of the protein
**** [[1ku6]] - mAChE + fasciculin 2 
**** [[1ku6]], [[1mah]] - mAChE + fasciculin 2 
**** [[1j07]] - mAChE + decidium 
**** [[1n5m]] - mAChE + gallamine 
**** [[1n5r]] - mAChE + propidium
**** [[1b41]], [[1f8u]] - hAChE + fasciculin 2 
**** [[1fss]] - TcAChE + fasciculin 2 
 
*** AChE bis inhibitors spanning the active site gorge
**** [[AChE bivalent inhibitors]]
**** [[3i6m]] – ''Tc''AChE + N-piperidinopropyl galanthamine 
**** [[3i6z]] - ''Tc''AChE + saccharinohexyl galanthamine 
**** [[1zgb]], [[1zgc]] – ''Tc''AChE + tacrine (10) hupyridone 
**** [[2w6c]] – ''Tc''AChE + bis-(-)-nor-meptazinol 
**** [[2ckm]], [[2cmf]] – ''Tc''AChE + bis-tacrine
**** [[2cek]] – ''Tc''AChE + N-[8-(1,2,3,4-tetrahydroacridin-9-ylthio)octyl]-1,2,3,4-tetrahydroacridin-9-amine 
**** [[1ut6]] - ''Tc''AChE + N-9-(1,2,3,4-tetrahydroacridinyl)-1,8-diaminooctane 
**** [[1odc]] - ''Tc''AChE + N-4-quinolyl-N-9-(1,2,3,4-tetrahydroacridinyl)-1,8-diaminooctane 
**** [[1w4l]], [[1w6r]], [[1w76]], [[1dx6]], [[1qti]] - TcAChE + galanthamine and derivative 
**** [[1q83]], [[1q84]] - mAChE + TZ2PA6 
**** [[1h22]], [[1h23]] – ''Tc''AChE + bis-hupyridone 
**** [[1hbj]] – ''Tc''AChE + quinoline derivativev
**** [[1e3q]] – ''Tc''AChE + bw284c51
**** [[1eve]] – ''Tc''AChE + e2020
**** [[1acl]] – ''Tc''AChE + decamethonium 
 
 
*** AChE organophosphate inhibitors causing irreversible inhibition
**** [[2wu3]] – mAChE + fenamiphos and HI-6
**** [[2wu4]] – mAChE + fenamiphos and ortho-7
**** [[2jgf]] - mAChE + fenamiphos
**** [[2wfz]], [[2wg0]], [[1som]] - ''Tc''AChE + soman
**** [[2wg1]] - ''Tc''AChE + soman + 2-PAM
**** [[2whp]], [[2whq]], [[2whr]] – mAChE + sarin and HI-6
**** [[2jgg]] - mAChE + sarin
**** [[2jgl]] - mAChE + VX and sarin
**** [[1cfj]] - ''Tc''AChE + sarin, GB
**** [[3dl4]], [[3dl7]] – mAChE + tabun
**** [[2jey]] – mAChE + HLO-7
**** [[2c0p]], [[2c0q]] - mAChE + tabun
**** [[2jez]] - mAChE + tabun + HLO-7
**** [[2jf0]] - mAChE + tabun + Ortho-7
**** [[2jgh]] - mAChE + VX
**** [[1vxo]], [[1vxr]] - ''Tc''AChE + VX
**** [[2jgi]], [[2jgm]] - mAChE + DFP
**** [[1dfp]] - ''Tc''AChE + DFP
**** [[2jgj]], [[2jgk]], [[2jge]] - mAChE + methamidophos
**** [[2gyu]] - mAChE + HI-6
**** [[2gyv]] - mAChE + Ortho-7
**** [[2gyw]] - mAChE + obidoxime
 
*** AChE substrate analogues mimicking the binding of the substrate acetylcholine
**** [[2ha4]] – mAChE (mutant) + acetylcholine
**** [[2vja]], [[2vjb]], [[2vjc]], [[2vjd]], [[2cf5]] – ''Tc''AChE + 4-oxo-N,N,N-trimethylpentanaminium
**** [[2v96]], [[2v97]], [[2v98]], [[2v99]] – ''Tc''AChE + 1-(2-nitrophenyl)-2,2,2-trifluoroethyl-arsenocholine
**** [[2ha2]] – mAChE + succinylcholine
**** [[2ha3]] - mAChE + choline
**** [[2ha5]] – mAChE (mutant) + acetylthiocholine
**** [[2ha6]] – mAChE (mutant) + succinylthiocholine
**** [[2ha7]] – mAChE (mutant) + butyrylthiocholine
**** [[2ch4]], [[2c58]] – ''Tc''AChE  + acetylthiocholine
**** [[2c5g]] – ''Tc''AChE  + thiocholine
 
*** Others…
**** [[2j4f]] – ''Tc''AChE + Hg
**** [[1vzj]] – ''Tc''AChE tetramerization domain
**** [[1jjb]] – ''Tc''AChE + PEG
 
** [[Acetylcholine binding protein]]  (AChBP)
** [[Butyrylcholinesterase]] (BChE)
** [[Glutamate receptor (GluA2)|Glutamate Receptor]]
 
 
* Prions and Intrinsically Disordered Proteins
** [[Prion protein]]
** [[Doppel]]
** [[Intrinsically Disordered Protein]]
 
* Small Iron Sulfur Proteins
** [[Ferredoxin]] (Fd)
*** 2Fe-2S containing ferredoxins
**** [[3hui]] – Fd – ''Rhodopseudomonas palustris''
**** [[2kaj]], [[1dox]], [[1doy]] – SyFd +Ga – Synechocystis – NMR
**** [[1off]] – SyFd 
**** [[3gce]] – Fd – Nocardioides aromaticivorans
**** [[2e4p]], [[2e4q]] - Fd – ''Pseudomonas sp.''
**** [[2q3w]], [[1vm9]] - PmFd (mutant) – ''Pseudomonas mendocina''
**** [[2i7f]] - Fd  – ''Rhodobacter capsulatus''
**** [[1rfk]] - Fd – Cyanobacterium ''masticogladus laminosus''
**** [[1vck]] - Fd – ''Pseudomonas resinovorans''
**** [[1wri]], [[1frr]] - Fd – Equisetum arvense
**** [[1sjg]] - PmFd– NMR
**** [[1iue]] - Fd– Plasmodium falciparum
**** [[1m2a]] –AeFd – Aquifex aeolicus
**** [[1m2b]], [[1m2d]], [[1f37]], [[1f5b]], [[1f5c]] – AeFd (mutant)
**** [[1l5p]] – Fd –  Trichomonas vaginalis
**** [[1i7h]] - Fd  – Escherichia coli
**** [[1czp]], [[1qt9]], [[1frd]], [[1fxa]] - aFd– anabaena
**** [[1j7a]], [[1j7b]], [[1j7c]] , [[1qoa]], [[1qob]], [[1qof]], [[1qog]]- aFd  (mutant) 
**** [[1e0z]] – Fd – Halobacterium salinarium
**** [[1pfd]] – Fd – Petroselinum crispum – NMR
**** [[1a70]] - Fd  (mutant) – Spinacia oleracea
**** [[1awd]] - Fd  – Chlorella fusca
**** [[2cjn]], [[2cjo]], [[1roe]] – SyFd – NMR
**** [[1rof]] – SyFd – Synechococcus elongates
**** [[1doi]] - Fd  – Haloarcula marismortui
**** [[4fxc]] – Fd – Spirulina platensis
**** [[1fxi]] – Fd – Aphanothece sacrum
**** [[3dqy]], [[2qpz]] - Fd  – Pseudomonas putida
 
*** 4Fe-4S containing ferredoxins
 
**** [[3eun]] – AvFd  – Allochromatium vinosum
**** [[3exy]] - AvFd (mutant)
**** [[2vkr]] - Fd+Zn – Acidianus ambivalens
**** [[2z8q]] - PfFd (mutant) – Pyrococcus furiosus
**** [[2fgo]] - Fd– Pseudomonas aeruginosa
**** [[1iqz]], [[1ir0]] - BtFd  – Bacillus thermoproteolyticus
**** [[1rgv]] - Fd  – Thauera aromatica
**** [[1dax]], [[1dfd]] – DaFd – Desulfovibrio africanus – NMR
**** [[1fxr]] - DaFd 
**** [[1vjw]] – Fd – Thermotoga maritima
 
*** 3Fe-4S containing ferredoxins
 
**** [[2v2k]] – Fd – Mycobacterium smegmatis
**** [[1wtf]] - BtFd (mutant) 
**** [[1sj1]] - PfFd 
**** [[1fxd]] - DgFd  – Desulfovibrio gigas
**** [[1f2g]] – DgFd – NMR
**** [[1xer]] - Fd  – Sulfolobus tokodaii
 
*** 4Fe-4S+3Fe-4S containing ferredoxins
 
**** [[1gao]], [[6fdr]], [[7fd1]], [[7fdr]], [[1axq]], [[6fd1]], [[1frh]], **** [[1fri]],[[1frj]], [[1frk]], [[1frl]], [[1frm]], [[1fda]], [[1fdb]], **** [[1fdd]], [[5fd1]], [[1fer]] – AvFd – Azotobacter vinelandii
**** [[1pc4]], [[1pc5]], [[1g6b]], [[1g3o]], [[1ff2]], [[1b0v]], [[1d3w]], **** [[1b0t]], [[1a6l]], [[1ftc]], [[1frx]], [[2fd2]], [[1fd2]] - AvFd  (mutant) 
**** [[1h98]] – Fd – Thermus thermophilus
**** [[1a8p]], [[1bd6]] - BsFd  – Bacillus schlegelii – NMR
 
*** 4Fe-4S+4Fe-4S containing ferredoxins
 
**** [[1dur]] – Fd – Peptoniphilus asaccarolyticus
**** [[1bwe]], [[1bqx]] - BsFd  (mutant) – NMR
**** [[2fdn]], [[1fca]] , [[1fdn]]- Fd – Clostridium acidi-urici
**** [[1blu]] - Fd – Chromatium vinosum
**** [[1clf ]]– Fd – Clostridium pasteurianum – NMR
 
*** Adrenoredoxin
 
**** [[2jqr]] – ADR Fd domain (mutant)+cytochrome c (mutant) – yeast – NMR
**** [[2bt6]] – cADR1 modified – cow
**** [[1l6u]], [[1l6v]] – cADR1 – NMR
**** [[1e6e]] – cADR (mutant)+ADR reductase
**** [[1cje]], [[1ayf]] - cADR
 
*** Putidaredoxin
 
**** [[1yji]], [[1yjj]], [[1pdx]] – PpPUT – Pseudomonas putida – NMR
**** [[3lb8]] – PpPUT (mutant)+PUT reductase
**** [[1xln]], [[1xlo]], [[1xlp]], [[1xlq]], [[1r7s]], [[1oqq]], [[1oqr]] - PpPUT (mutant)
**** [[1gpx]], [[1put]]- PpPUT (mutant) - NMR
 
*** Terpredoxin
 
**** [[1b9r]] – TER – Pseudomonas - NMR
 
 
* Toxins
** [[Pore forming toxin, α-hemolsyin|The pore forming toxin, &#945;-hemolsyin]]
** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
 
 
* Diseases
** Cancer
*** [[SRC]]
*** [[Proteins involved in cancer]]
 
* Evolution
** [[Conservation, Evolutionary]]
** [[Extremophiles]]
 
* 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
* Gene Expression & Replication
*** [[1fnm|Ef-G]]
** [[DNA Replication]]
*** [[Ribosome]]
** [[Nucleic Acids]]
*** [[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit]]
** [[Regulation of Gene Expression]]
*** [[Ribosomal back translocase|ribosomal back translocase, Escherichia coli LepA]]
** [[RNAi]]
*** [[SelB Recognition]]
** [[Transcription & RNA Processing]]
*** [[1ehz|tRNA]]
** [[Translation]]  


** Regulation of Gene Expression
* Large Macromolecular Assemblies
*** [[Lac repressor]]
** [[Group:MUZIC|Muscle sarcomere: Z-Disk]]
*** [[Irr]] (Iron Response Regulator )
** [[Ribosome]]
*** Oncogenes
** [[Ribosoma 70S]]
**** [[P53]]
** [[Nucleosomes]]
**** [[SRC]]
** [[Nucleosome structure]]
*** [[Tangible Models of Cdc42 Interacting With Intersectin]]
 
* Immune System
** Antibodies
*** [[IgA]]
*** [[Epitopes]]
** [[Major Histocompatibility Complex Class I]]
*** [[Human beta two microglobulin]]


* Metabolism
* Metabolism
** Introduction to Metabolism
** [[Amino Acid Synthesis & Metabolism]]
 
** [[Carbohydrate Metabolism]]
** Glucose Catabolism
** [[Photosynthesis]]
*** [[Triose Phosphate Isomerase]]
** [[Regulation of Gene Expression]]
***[[Phosphofructokinase %28PFK%29]]
** [[Drug Metabolism by CYP450 Enzymes]]
 
 
** 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]]
 
 
 
* 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
**** [[S347/Visualising protein structure|Visualising Protein Structure]] - Introduction to Jmol
**** [[FirstGlance in Jmol]]
*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
*** Homology Model
**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
**** [[User:Emi Nakayama/TRIM5a Homology Models|TRIM5a Homology Models]] - Differences in models as a function of their templates
*** [[DRuMS]] - set of standard color schemes for macromolecular visualization
 
** Sequence Analysis
*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]
 
* Model Structures
** See [[Theoretical models]]
** [[African Malaria Mosquito Acetylcholinesterase]]
** [[Structure of E. coli DnaC helicase loader]]
** [[User:Yuan-Ping Pang/HAB•BoNTAe]]


* Miscellaneous
* Miscellaneous
** [[Molecular Playground]]
** [[Colored & Bioluminescent Proteins]]
** [[Research Groups]]
** [[Coronavirus Disease 2019 (COVID-19)]]
}}
** [[Enzimas: complejo enzima-sustrato]]
</big>
** [[3D Molecular Models]]
 
** [[Metal-Organic Framework]]
{{Clear}}
** [[Metal-Ligand Polyhedra]]
 
==Alphabetical Index==


[[Image: Picture_15.png|520px|right|thumb]]
* Signaling & Transport
{{#tree:id=alphabeticalIndex|openlevels=1|close=top|open=top|
** [[Hormone]]
** A
** [[Membrane Channels & Pumps]]
*** [[Acetylcholinesterase]]
*** [[Aconitase]]
*** [[Actin]]
*** [[ABC transporter]]
*** [[Actinin]]
*** [[Adenylyl cyclase]]
*** [[Adrenodoxin]]
*** [[Agrin]]
*** [[Angiotensin-Converting Enzyme]]
*** [[Annexin]]
*** [[Aquaporin]]
*** [[ATPase]]
*** [[Avidin]]
** B
*** [[Butyrylcholinesterase]]
*** [[BPTI]] (Basic Pancreatic Trypsin Inhibitor)
** C
*** [[Cadherin]]
*** [[Calmodulin]]
*** [[Ca2+/Calmodulin-dependent kinase]]
*** [[Catenin]]
*** [[Cystic Fibrosis Transmembrane regulator]]
*** [[Chymotrypsin]]
*** [[Chymotrypsin inhibitor 2]]
*** [[Cyclophilin]]
*** [[Cytochrome P450]]
** D
*** [[Dihydrofolate Reductase]]
** E
*** [[EGFR]]
*** [[Eglin]]
*** [[Elastase]]
*** [[Endoplasmin]]
** F
*** [[Ferredoxin]]
*** [[Ferritin]]
*** [[Fibrin]]
*** [[Fibrinogen]]
*** [[Fibronectin]]
*** [[Filamin]]
*** [[Flavodoxin]]
*** [[Filamenting Temperature-Sensitive Mutant Z]]
** G
*** [[Gelsolin]]
*** [[Gyrase]]
** H
*** [[Heat shock protein]]
*** [[Hirudin]]
** I
** J
** K
*** [[Kinesin]]
** L
*** [[Lipase]]
** M
*** [[Malate Dehydrogenase]]
*** [[Myoglobin]]
*** [[Myosin]]
** N
*** [[Nucleoporin]]
** O
** P
*** [[Potassium, Calcium Channel]]
*** [[Porin]]
** Q
** R
*** [[RecA]]
*** [[Resolvase]]
*** [[Reverse Transcriptase]]
** S
*** [[Severin]]
*** [[Spectrin]]
*** [[Strepavidin]]
*** [[Subtilisin]]
*** [[Superoxide Dismutase]]
*** [[Superoxide reductase]]
** T
*** [[Talin]]
*** [[TATA-binding protein]]
*** [[Telethonin]]
*** [[Telomerase]]
*** [[Thioredoxin]]
*** [[Titin]]
*** [[Topoisomerase]]
*** [[Tropomyosin]]
*** [[Troponin]]
*** [[Tubulin]]
** U
*** [[Ubiquitin]]
** V
*** [[Villin]]
*** [[Vinculin]]
** W
** X
** Y
** Z


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