The assembly of biological molecules, most notably globular proteins1 and RNA,2,3 into unique threedimensional structures with well-defined topology is a complex and fascinating phenomenon in molecular biology. There are two aspects to the problem of folding of proteins and RNA. The first is the prediction of the three-dimensional structure of the folded state from the one-dimensional primary s...

RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires RNA tertiary structure knowledge. Although modeling approaches for the study of RNA structures and dynamics lag behind efforts in protein folding, much progress has been achieved in the past two years. Here, we review recent advances in ...

RNA folding is viewed here as a map assigning secondary structures to sequences. At fixed chain length the number of sequences far exceeds the number of structures. Frequencies of structures are highly non-uniform and follow a generalized form of Zipf's law: we find relatively few common and many rare ones. By using an algorithm for inverse folding, we show that sequences sharing the same struc...

In this paper I outline a fast method called KFOLD for implementing the Gillepie algorithm to stochastically sample the folding kinetics of an RNA molecule at single base-pair resolution. In the same fashion as the KINFOLD algorithm, which also uses the Gillespie algorithm to predict folding kinetics, KFOLD stochastically chooses a new RNA secondary structure state that is accessible from the c...

We analyze the distribution of RNA secondary structures given by the Knudsen-Hein stochastic context-free grammar used in the prediction program Pfold. Our main theorem gives relations between the expected number of these motifs--independent of the grammar probabilities. These relations are a consequence of proving that the distribution of base pairs, of helices, and of different types of loops...

The rugged nature of the RNA folding landscape is determined by a number of conflicting interactions like repulsive electrostatic potential between the charges on the phosphate groups, constraints due to loop entropy, base stacking, and hydrogen bonding that operate on various length scales. As a result the kinetics of self-assembly of RNA is complex, but can be easily modulated by varying the ...

MOTIVATION The need for accurate and efficient tools for computational RNA structure analysis has become increasingly apparent over the last several years: RNA folding algorithms underlie numerous applications in bioinformatics, ranging from microarray probe selection to de novo non-coding RNA gene prediction. In this work, we present RAF (RNA Alignment and Folding), an efficient algorithm for ...