Biomedical Engineering Reference
In-Depth Information
1.2
MODELING RNA FOLDING
Ivo L. Hofacker
Institute for Theoretical Chemistry and Structural Biology,
University of Vienna
Peter F. Stadler
Bioinformatics, Department of Computer Science,
University of Leipzig, Leipzig, Germany
In recent years it has become evident that functional RNAs in living organisms are not
just curious remnants from a primordial RNA world but a ubiquitous phenomenon com-
plementing protein enzyme based activity. Functional RNAs, just like proteins, depend in
many cases upon their well-defined and evolutionarily conserved three-dimensional
structure. In contrast to protein folds, however, RNA molecules have a biophysically im-
portant coarse-grained representation: their secondary structure. At this level of resolu-
tion at least, RNA structures can be efficiently predicted given only the sequence
information. As a consequence, computational studies of RNA routinely incorporate
structural information explicitly. RNA secondary structure prediction has proven useful
in diverse fields, ranging from theoretical models of sequence evolution and biopolymer
folding, to genome analysis, and even the design of biotechnologically or pharmaceuti-
cally useful molecules. Properties such as the existence of neutral networks or shape
space covering are emergent properties determined by the complex, highly nonlinear rela-
tionship between RNA sequences and their structures.
1.
INTRODUCTION
It is not hard to argue that
RNomics
, i.e., an understanding of functional
RNAs (both ncRNA genes and functional motifs in protein-coding RNAs) and
Address correspondence to: Peter F. Stadler, Department of Computer Science, University of Leip-
zig, Härtelstrasse 16-18, Leipzig, D-04107 Germany (peter.stadler@bioinf. uni-leipzig.de)
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