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{{#tree:id=siteTree|openlevels=1|root='''Chemistry of Life'''|
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)


* INTRODUCTION
'''When you create a new page in Proteopedia, please add it to corresponding topic subpages.'''
** Introduction to the Chemistry of Life
** Water
*** [[Water_in_macromolecular_models]]
** Key chemical concepts for Structural Biology
*** [[Cation-pi interactions]]


* BIOMOLECULES
==Topics Pages Organized by Category==
** Nucleotides, Nucleic Acids, and Genetic Information
{{#tree:id=OrganizedByTopic|openlevels=0|
*** [[DNA]]
**** [[Z-DNA]]
** [[Amino_Acids]]
** Proteins: Primary Structure
** Proteins: Three-Dimensional Structure
** Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
*** [[Calmodulin_in_motion]]
*** [[Collagen]]
** DNA BINDING PROTEINS
*** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]
** COLORED PROTEINS & THOSE THAT CHANGE COLOR
*** [[Dronpa]]
** Lipids and Biological Membranes
** Membrane Transport
*** [[A Physical Model of the β2-Adrenergic Receptor]]
** Prions & Intrinsically Disordered Proteins
*** [[Doppel]]


* ENZYMES
* [[Introduction to protein structure]] - A introductory overview of protein structure.
** Enzymatic Catalysis
* [[About Macromolecular Structure]] - List of pages about macromolecular structure terms and concepts.
*** [[Aconitase]]
* [[Proteopedia:Topic Pages|Topic pages]] - List of pages about specific proteins or protein families.
*** Serine Hydrolases
* [[Index pages]] - List of pages that list other pages within Proteopedia.
**** [[Acetylcholinesterase]] (AChE)
* Basics of Protein Structure
***** [[Acetylcholine]]
**[[Introduction to protein structure]] - A introductory overview of protein structure
***** [[Flexibility_of_aromatic_residues_in_acetylcholinesterase]]
**[[Proteins: primary and secondary structure]]
***** [[AChE inhibitors and substrates]]
**[[Myoglobin of Physeter catodon: structure]]
****** [[1eve]] AChE-Aricept complex
** The Building Blocks
****** [[AChE_bivalent_inhibitors]]
*** [[Amino Acids]]
***[[Triose_Phosphate_Isomerase]]
*** [[Backbone_representations]]
** Enzyme Kinetics, Inhibition, and Control
*** [[Peptide]]
** Biochemical Signaling
**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]


* METABOLISM
** Conformational flexibility of a polypeptide chain
** Introduction to Metabolism
*** [[Phi and Psi Angles]]
** Glucose Catabolism
*** [[Ramachandran Plots]]
** Glycogen Metabolism and Gluconeogenesis
*** [[Tutorial:Ramachandran principle and phi psi angles]]
** Citric Acid Cycle
** [[Secondary structure]]
** Electron Transport and Oxidative Phosphorylation
*** [[Helices in Proteins]]
** Photosynthesis
**** [[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
** Lipid Metabolism
*** [[Sheets in Proteins]]
** Amino Acid Metabolism
**** [[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]]
** Mammalian Fuel Metabolism: Integration and Regulation
** [[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]]


* GENE EXPRESSION AND REPLICATION
** Nucleotide Metabolism
** Nucleic Acid Structure
** DNA Replication, Repair, and Recombination
*** [[DNA Replication,Transcription and Translation]]
** Transcription and RNA Processing
** Protein Synthesis
** Regulation of Gene Expression


* METHODS OF STRUCTURE DETERMINATION
** [[Unusual Motifs in Proteins]]
** X-ray
*** [[Cation-pi_interactions]]
***[[X-ray_crystallography]]
*** [[Thermal_motion_of_peptide]]
****[[Asymmetric_Unit]]
****[[Biological_Unit]]
****[[Electron_density_maps]]
***SAXS
** NMR
** Electron Microscopy


* METHODS OF STRUCTURE & SEQUENCE ANALYSIS 
** [[Intrinsically Disordered Protein]]
** STRUCTURAL ANALYSIS & VISUALIZATION
 
*** [[Chime]]
* Carbohydrates
*** [[User:Wayne Decatur/Teaching Proteopedia]]
**[[Carbohydrates]]
*** [[User:Wayne Decatur/Homology Modeling]]
**[[Carbohydrates II]]
*** [[User:Wayne Decatur/Generate Unfolded Structures]]
* Cytoskeletal Proteins
*** [[DRuMS]] - set of standard color schemes for macromolecular visualization
** [[Actin]]
** SEQUENCE ANALYSIS
** [[Keratins]]
*** [[User:Wayne Decatur/Sequence analysis tools]]
** [[Tropomyosin]]
** [[Tubulin]]
 
* Lipids
**[[Lipids: structure and classification]]
 
* Diseases & Related Topics
** [[Alzheimer's Disease]]
** [[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
** [[Hydrolases]]
** [[Isomerases]]
** [[Ligases]]
** [[Lyases]]
** [[Oxidoreductases]]
** [[Transferases]]
 
* Gene Expression & Replication
** [[DNA Replication]]
** [[Nucleic Acids]]
** [[Regulation of Gene Expression]]
** [[RNAi]]
** [[Transcription & RNA Processing]]
** [[Translation]]  
 
* Large Macromolecular Assemblies
** [[Group:MUZIC|Muscle sarcomere: Z-Disk]]
** [[Ribosome]]
** [[Ribosoma 70S]]
** [[Nucleosomes]]
** [[Nucleosome structure]]
 
* Metabolism
** [[Amino Acid Synthesis & Metabolism]]
** [[Carbohydrate Metabolism]]
** [[Photosynthesis]]
** [[Regulation of Gene Expression]]
** [[Drug Metabolism by CYP450 Enzymes]]
 
* Miscellaneous
** [[Colored & Bioluminescent Proteins]]
** [[Coronavirus Disease 2019 (COVID-19)]]
** [[Enzimas: complejo enzima-sustrato]]
** [[3D Molecular Models]]
 
* Signaling & Transport
** [[Hormone]]
** [[Membrane Channels & Pumps]]


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Latest revision as of 01:18, 31 December 2021

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: 31-12-2021 (DD-MM-YYYY)

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

Topics Pages Organized by Category


Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, Joel L. Sussman, Judy Voet, Eran Hodis, Tilman Schirmer, Eric Martz, Yuan-Ping Pang, Wayne Decatur, Helen Ginn, David Canner, Alexander Berchansky, Angel Herraez, Karl Oberholser, Tomas Klumpler, Arthur Cox, Karen L. Lee, Israel Hanukoglu, Alejandro Porto
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