Grammatical representations of macromolecular structure.
Since the first application of context-free grammars to RNA secondary structures in 1988, many researchers have used both ad hoc and formal methods from computational linguistics to model RNA and protein structure. We show how nearly all of these methods are based on the same core principles and can be converted into equivalent approaches in the framework of tree-adjoining grammars and related formalisms. We also propose some new approaches that extend these core principles in novel ways.
Chiang
David
D
Information Sciences Institute, University of Southern California, Marina del Rey, California 90292, USA. chiang@isi.edu
Joshi
Aravind K
AK
Searls
David B
DB
D000465:Algorithms; D019295:Computational Biology; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA