Contents

• Introduction
  • The Biology Story
  • The Informatics Story
  • The New MC-Sym
  • MC-Sym III: A new approach
    • Fragment Generators
    • The Fragment Generator hierarchy
    • Constraint objects
    • Related Work
  
  
• Installation
• The annotation process
  • Local referentials and homogeneous transformation matrices
  • Nucleotide conformations
  • Base-base interactions
  • Base pairing
  • Base stacking
  
  
• Commands reference
  • Sequence description
    • sequence
  • Conformation
    • residue
  • Relations between nucleotides
    • connect
    • pair
  • Building information
    • backtrack
    • cache
    • library
  • Constraints
    • Adjacency
    • Angle
    • Residue clash
    • Distance
    • Relation
    • Torsion
  • Exploration of the conformational space
    • explore
    • exploreLV
  • Miscellaneous commands
    • source
    • restore
    • notes
    • remark
    • reset
    • version
    • quit
    • Comments
  
  
• Database properties reference
  • Properties
  • Conformational properties of the residue
  • Properties of the relation between two residues
  
  
• A complete example: The tRNA Anticodon stem loop Script
• Base pairings classification
• Bibliography
• Index