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==INTRODUCTION==
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 to the Chemistry of Life
 
* Water
'''When you create a new page in Proteopedia, please add it to corresponding topic subpages.'''
** [[Water_in_macromolecular_models]]
 
* Key chemical concepts for Structural Biology
==Topics Pages Organized by Category==
** [[Cation-pi interactions]]
{{#tree:id=OrganizedByTopic|openlevels=0|
 
* [[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]]
*** [[Backbone_representations]]
*** [[Peptide]]
**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
 
** Conformational flexibility of a polypeptide chain
*** [[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]]
 
 
** [[Unusual Motifs in Proteins]]
*** [[Cation-pi_interactions]]
*** [[Thermal_motion_of_peptide]]
 
** [[Intrinsically Disordered Protein]]


==BIOMOLECULES==
* Nucleotides, Nucleic Acids, and Genetic Information
**[[Z-DNA]]
* [[Amino_Acids]]
* Proteins: Primary Structure
* Proteins: Three-Dimensional Structure
* Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
**[[Calmodulin_in_motion]]
* Carbohydrates
* Carbohydrates
* Lipids and Biological Membranes
**[[Carbohydrates]]
* Membrane Transport
**[[Carbohydrates II]]
**[[A Physical Model of the β2-Adrenergic Receptor]]
* Cytoskeletal Proteins
** [[Actin]]
** [[Keratins]]
** [[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]]  


==ENZYMES==
* Large Macromolecular Assemblies
* Enzymatic Catalysis
** [[Group:MUZIC|Muscle sarcomere: Z-Disk]]
** [[Aconitase]]
** [[Ribosome]]
** Serine Hydrolases
** [[Ribosoma 70S]]
*** [[Acetylcholinesterase]] (AChE)
** [[Nucleosomes]]
**** [[Acetylcholine]]
** [[Nucleosome structure]]
**** [[Flexibility_of_aromatic_residues_in_acetylcholinesterase]]
**** [[AChE inhibitors and substrates]]
***** [[1eve]] AChE-Aricept complex
***** [[AChE_bivalent_inhibitors]]
**[[Triose_Phosphate_Isomerase]]
* Enzyme Kinetics, Inhibition, and Control
* Biochemical Signaling


==METABOLISM==
* Metabolism
* Introduction to Metabolism
** [[Amino Acid Synthesis & Metabolism]]
* Glucose Catabolism
** [[Carbohydrate Metabolism]]
* Glycogen Metabolism and Gluconeogenesis
** [[Photosynthesis]]
* Citric Acid Cycle
** [[Regulation of Gene Expression]]
* Electron Transport and Oxidative Phosphorylation
** [[Drug Metabolism by CYP450 Enzymes]]
* Photosynthesis
* Lipid Metabolism
* Amino Acid Metabolism
* Mammalian Fuel Metabolism: Integration and Regulation


== GENE EXPRESSION AND REPLICATION ==
* Miscellaneous
* Nucleotide Metabolism
** [[Colored & Bioluminescent Proteins]]
* Nucleic Acid Structure
** [[Coronavirus Disease 2019 (COVID-19)]]
* DNA Replication, Repair, and Recombination
** [[Enzimas: complejo enzima-sustrato]]
* Transcription and RNA Processing
** [[3D Molecular Models]]
* Protein Synthesis
* Regulation of Gene Expression


== METHODS OF STRUCTURE DETERMINATION ==
* Signaling & Transport
* X-ray
** [[Hormone]]
**[[X-ray_crystallography]]
** [[Membrane Channels & Pumps]]
***[[Asymmetric_Unit]]
***[[Biological_Unit]]
**SAXS
* NMR
* Electron Microscopy


== METHODS OF STRUCTURE & SEQUENCE ANALYSIS  ==
}}
* STRUCTURAL ANALYSIS & VISUALIZATION
__NOTOC__
**[[User:Wayne Decatur/Teaching Proteopedia]]
__NOEDITSECTION__
**[[User:Wayne Decatur/Homology Modeling]]
**[[User:Wayne Decatur/Generate Unfolded Structures]]
*SEQUENCE ANALYSIS
**[[User:Wayne Decatur/Sequence analysis tools]]
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