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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)


<big>
'''When you create a new page in Proteopedia, please add it to corresponding topic subpages.'''
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* Introduction to Structural Biology
==Topics Pages Organized by Category==
** See [[About Macromolecular Structure]]
{{#tree:id=OrganizedByTopic|openlevels=0|
** 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]]


** Amino Acids
** [[Unusual Motifs in Proteins]]
*** [[Amino Acids]]
*** [[Cation-pi_interactions]]
*** [[Selenocysteine]]
*** [[Thermal_motion_of_peptide]]
** Proteins, Primary Structure
*** [[Conservation, Evolutionary]]
*** [[Isoelectric point]]


** Proteins, Three-Dimensional Structure
** [[Intrinsically Disordered Protein]]
*** [[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]]
 
** 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
* Carbohydrates
*** [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
**[[Carbohydrates]]  
*** Filamentous bacteriophage
**[[Carbohydrates II]]
**** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage
* Cytoskeletal Proteins
*** HIV
** [[Actin]]
**** [[HIV-1 protease]]
** [[Keratins]]
**** [[HIV-1 Gag]]
** [[Tropomyosin]]
**** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
** [[Tubulin]]
**** [[User:Eric Martz/Molecular Playground/HIVDrug]]
*** Herpes Simplex Virus
**** [[Herpes Simplex Virus Thymidine Kinase]]
*** Influenza
**** [[Influenza hemagglutinin]]
**** [[Avian Influenza Neuraminidase, Tamiflu and Relenza]]


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


* Colored Proteins & those that Change Color
* Diseases & Related Topics
** [[Green Fluorescent Protein]]; [[GFP (Hebrew)]]
** [[Alzheimer's Disease]]
** [[Dronpa]]
** [[Antibody]]
** [[Factor IX]]
** [[Bacterial Infections]]
 
** [[Cancer]]
 
** [[Coronavirus Disease 2019 (COVID-19)]]
* DNA Binding Proteins
** [[Diabetes & Hypoglycemia]]
** [[Helix-turn-helix motif]]
** [[Hemophilia]]
** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]
** [[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]]
** [[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)
 
 
* 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
* Gene Expression & Replication
*** [[DNA Replication,Transcription and Translation]]
** [[DNA Replication]]
*** [[DNA Polymerase I]]
** [[Nucleic Acids]]
*** [[PcrA helicase]]
** [[Regulation of Gene Expression]]
*** [[Fpg Nei Protein Superfamily]] - DNA Repair and Base Excision DNA Repair
** [[RNAi]]
*** [[Human RecQ-Like protein 1]] - RecQ family of DNA helicases are conserved in from bacteria to man
** [[Transcription & RNA Processing]]
*** [[Structure of E. coli DnaC helicase loader]]
** [[Translation]]  
*** [[1x9n#Crystal Structure of Human DNA Ligase I bound to 5.27-adenylated.2C nicked DNA]]
*** [[Rop protein]]


** Transcription and RNA Processing
* Large Macromolecular Assemblies
*** T-box family
** [[Group:MUZIC|Muscle sarcomere: Z-Disk]]
**** [[T-box proteins]]
** [[Ribosome]]
**** [[Brachyury]]
** [[Ribosoma 70S]]
**** [[TBX1]]
** [[Nucleosomes]]
**** [[TBX15]]
** [[Nucleosome structure]]
*** [[C-Myc]]
*** [[Lac repressor]]
*** [[Reverse transcriptase]]
*** [[TATA-Binding Protein]]
*** [[RSP1275]]
*** [[Transcription Termination Factor Rho]]
 
** Protein Synthesis
*** [[Ribosome]]
*** [[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit]]
*** [[SelB Recognition]]
** 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]]


* Metabolism
* Metabolism
** Introduction to Metabolism
** [[Amino Acid Synthesis & Metabolism]]
** [[Carbohydrate Metabolism]]
** [[Photosynthesis]]
** [[Regulation of Gene Expression]]
** [[Drug Metabolism by CYP450 Enzymes]]


** 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
** [[Metal-Organic Framework]]
*** [[Phosphoglucose isomerase]]
** [[Metal-Ligand Polyhedra]]
*** [[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]]


* Signaling & Transport
** [[Hormone]]
** [[Membrane Channels & Pumps]]


* 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
** [[Molecular Playground]]
** [[Research Groups]]
}}
}}
</big>
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Latest revision as of 19:52, 9 October 2025

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. Updated: 09-10-2025 (DD-MM-YYYY)

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