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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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