Lecture 5
Modeling RNA three-dimensional structure
	Models vs structures - but even Xray & NMR structures are models
	Resolution - helix vs residue vs atomic
	3D structure implicit in secondary structures
		i.e. secondary is not 2 dimensional!
		helices - A form RNA
		motifs - e.g. tetraloops
	3D vs 4D
		RNAs are dynamic
		compare RNA machines with a machine - car engine
	Global vs regional models
	Data - constraints needed!
		Secondary structure
			phylogenetic
			genetic
			SELEX
			variation data
			pseudoknots - very constraining
		structure probing
		X-linking
		base mods
		physical data
		
	Interactive computer graphics - manual - Westhof/Massire
		~ wire model building
		extension of the comparative approach
		examples
		strengths
		weaknesses
		can you use it?
		The most productive method to date
	MC-SYM
		search for all geometrically possible solutions via brute force
		the algorithm
		the data
		results
		strengths
		weaknesses
		when to use it
	Molecular mechanics - e.g.YAMMP
		principle
		the algorithm
		the data
		results
		strengths
		weaknesses
		when to use it
	Discrete vs probablistic modeling
	Evaluation of models