structural

name	structural
description	Structural biology fundamentals
license	MIT
compatibility	opencode
metadata	{"audience":"biologists, students, researchers","category":"biology"}

What I do

• Explain molecular structure principles
• Describe protein structure organization
• Discuss structural analysis methods
• Analyze molecular interactions
• Connect structure to function
• Explain structural determination techniques

When to use me

• When learning structural biology basics
• When explaining protein structure
• When studying molecular interactions
• When preparing educational content

Key Concepts

Biomolecular Structure

Proteins

• Amino acids linked by peptide bonds
• 20 standard amino acids
• Primary through quaternary structure
• Folding into 3D conformation

Nucleic Acids

• DNA: Double helix (B-form)
• RNA: Various structures (A, Z, hairpins)
• Nucleotides: Phosphate-sugar-base

Molecular Interactions

# Common interactions
interactions = {
    'covalent': 'Strong, ~350 kJ/mol, shared electrons',
    'ionic': 'Moderate, ~250 kJ/mol, charge-charge',
    'hydrogen': 'Weak-moderate, ~20-40 kJ/mol, X-H---Y',
    'hydrophobic': 'Weak, ~5 kJ/mol, entropy-driven',
    'van_der_waals': 'Very weak, ~1 kJ/mol, induced dipoles'
}

# Bond types in biomolecules
bonds = {
    'peptide': 'N-C, backbone',
    'glycosidic': 'Sugar-sugar, sugar-base',
    'phosphodiester': 'Nucleotide backbone'
}

Techniques Overview

• X-ray crystallography
• NMR spectroscopy
• Cryo-EM
• Mass spectrometry
• Spectroscopy (UV, CD, fluorescence)
• Computational modeling

Structure Databases

• PDB: Protein Data Bank
• NCBI Structure
• EMDB: Electron Microscopy DB
• AlphaFold DB