Proteopedia:Table of Contents
From Proteopedia
Revision as of 01:14, 19 September 2010 by Eran Hodis (talk | contribs) (Table of Contents moved to Proteopedia:Table of Contents)
Contents
This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the search slots at the left if you don't find what you are looking for below.
When 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.
Index by Topic
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- Introduction to Structural Biology
- See About Macromolecular Structure
- Water
- Key Chemical Concepts for Structural Biology
- Biomolecules
- About Macromolecular Structure
- Nucleotides, Nucleic Acids and Genetic Information
- DNA
- RNA
- RNA
- RNA motifs
- Amino Acids
- Proteins, Primary Structure
- Proteins, Three-Dimensional Structure
- Colored Proteins & those that Change Color
- DNA Binding Proteins
- Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
- Lipids and Biological Membranes
- Lipid Binding Proteins
- Membrane Transport Proteins
- Prions and Intrinsically Disordered Proteins
- Toxins
- Mitosis, Meiosis and Cargo Transport Proteins
- Viruses
- Suppression of RNA Silencing by Viruses
- Filamentous bacteriophage
- G3p - minor coat protein found on the surface of filamentous bacteriophage
- HIV
- Herpes Simplex Virus
- Influenza
- Colored Proteins & those that Change Color
- DNA Binding Proteins
- Enzymes
- Enzymatic Catalysis
- Acid-beta-glucosidase
- Acid Proteases
- Aconitase
- Cysteine Proteases
- Hen Egg-White (HEW) Lysozyme
- Choline Oxidase
- Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
- Metalloproteases
- Oxidoreductases
- Phosphofructokinase (PFK)
- Pyruvate phosphate dikinase
- Serotonin N-acetyltransferase
- Serine Hydrolases
- Serine Protease
- Triose Phosphate Isomerase
- Enzyme Inhibitors
- Enzyme Kinetics, Inhibition, and Control
- Biochemical Signaling
- Enzymes - Molecular Machines
- Enzymatic Catalysis
- Fibrous Proteins
- Membrane Transport Proteins
- Myoglobin & Hemoglobin
- 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 – TcAChE – trigonal – Torpedo californica
- 2j3d – TcAChE – monoclinic
- 1w75 – TcAChE – orthorhombic
- 1eea – TcAChE – cubic
- 2vt6, 2vt7 – TcAChE – different dosage
- 1qid to 1qim - TcAChE synchrotron radiation damage
- 1j06, 1maa – mAChE - mouse
- 1qo9 – DmAChE - Drosophila
- 1c2o, 1c2b – electrophorus AChE – Electric eel
- AChE active site inhibitors conjugating at the bottom of the active site gorge
- 2w9i – TcAChE + methylene blue
- 2wls – MosAChE + AMTS13
- 2vq6 – TcAChE + 2-PAM
- 2j3q – TcAChE + Thioflavin T
- 2ha0 – mAChE + ketoamyltrimethylammonium
- 2h9y – mAChE + TMTFA
- 1gpk, 1gpn, 1vot – TcAChE + huperzine
- 1gqr – TcAChE + rivastigmine
- 1gqs – TcAChE + NAP
- 1e66 – TcAChE + huprine
- 1dx4, 1qon – DmAChE + tacrine derivative
- 1oce – TcAChE + MF268
- 1ax9, 1ack – TcAChE + edrophonium
- 1amn – TcAChE + TMTFA
- 1acj – TcAChE + tacrine
- AChE peripheral site inhibitors conjugating at the surface of the protein
- AChE bis inhibitors spanning the active site gorge
- AChE bivalent inhibitors
- 3i6m – TcAChE + N-piperidinopropyl galanthamine
- 3i6z - TcAChE + saccharinohexyl galanthamine
- 1zgb, 1zgc – TcAChE + tacrine (10) hupyridone
- 2w6c – TcAChE + bis-(-)-nor-meptazinol
- 2ckm, 2cmf – TcAChE + bis-tacrine
- 2cek – TcAChE + N-[8-(1,2,3,4-tetrahydroacridin-9-ylthio)octyl]-1,2,3,4-tetrahydroacridin-9-amine
- 1ut6 - TcAChE + N-9-(1,2,3,4-tetrahydroacridinyl)-1,8-diaminooctane
- 1odc - TcAChE + 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 – TcAChE + bis-hupyridone
- 1hbj – TcAChE + quinoline derivativev
- 1e3q – TcAChE + bw284c51
- 1eve – TcAChE + e2020
- 1acl – TcAChE + 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 - TcAChE + soman
- 2wg1 - TcAChE + soman + 2-PAM
- 2whp, 2whq, 2whr – mAChE + sarin and HI-6
- 2jgg - mAChE + sarin
- 2jgl - mAChE + VX and sarin
- 1cfj - TcAChE + 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 - TcAChE + VX
- 2jgi, 2jgm - mAChE + DFP
- 1dfp - TcAChE + 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 – TcAChE + 4-oxo-N,N,N-trimethylpentanaminium
- 2v96, 2v97, 2v98, 2v99 – TcAChE + 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 – TcAChE + acetylthiocholine
- 2c5g – TcAChE + thiocholine
- Others…
- Acetylcholine binding protein (AChBP)
- Butyrylcholinesterase (BChE)
- Glutamate Receptor
- Acetylcholinesterase (AChE)
- Prions and Intrinsically Disordered Proteins
- 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
- 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
- Adrenoredoxin
- Putidaredoxin
- Terpredoxin
- 1b9r – TER – Pseudomonas - NMR
- 2Fe-2S containing ferredoxins
- Ferredoxin (Fd)
- Toxins
- Diseases
- Cancer
- Evolution
- Gene Expression and Replication
- Nucleic Acid Structure
- 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
- Protein Synthesis
- Regulation of Gene Expression
- Lac repressor
- Irr (Iron Response Regulator )
- Oncogenes
- Tangible Models of Cdc42 Interacting With Intersectin
- Immune System
- Metabolism
- Introduction to Metabolism
- Glucose Catabolism
- Glycogen Metabolism and Gluconeogenesis
- Citric Acid Cycle
- Electron Transport and Oxidative Phosphorylation
- Photosynthesis
- Lipid Metabolism
- Amino Acid Metabolism
- Mammalian Fuel Metabolism: Integration and Regulation
- Nucleotide Metabolism
- Methods of Structure Determination
- X-ray
- NMR
- Electron Microscopy
- Methods of Structure & Sequence Analysis
- Structural Analysis & Visualization
- CPK - Corey-Pauling-Koltun spacefilling molecular models and color scheme for elements
- Chime
- Jmol
- Visualising Protein Structure - Introduction to Jmol
- FirstGlance in Jmol
- Teaching Proteopedia
- Generate Unfolded Structures
- Homology Model
- Homology Modeling
- TRIM5a Homology Models - Differences in models as a function of their templates
- DRuMS - set of standard color schemes for macromolecular visualization
- Sequence Analysis
- Structural Analysis & Visualization
- Model Structures
- Miscellaneous
Alphabetical Index
(incomplete -- still in development as of Sept 18 2010. Missing many pages from the above Index by Topic and from Proteopedia:Interesting_Pages)
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- A
- B
- Butyrylcholinesterase
- BPTI (Basic Pancreatic Trypsin Inhibitor)
- C
- D
- E
- F
- G
- H
- I
- J
- K
- L
- M
- N
- O
- P
- Q
- R
- S
- T
- U
- V
- W
- X
- Y
- Z
Proteopedia Page Contributors and Editors (what is this?)
Joel L. Sussman, Judy Voet, Alexander Berchansky, Eran Hodis, Jaime Prilusky, Wayne Decatur, Eric Martz, Alejandro Porto, Angel Herraez, Karen L. Lee, Helen Ginn, Karl Oberholser, Israel Hanukoglu, Arthur Cox, Yuan-Ping Pang, Tilman Schirmer, Tomas Klumpler, David Canner
