Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Prediction and statistics of pseudoknots in RNA structures using exactly
  clustered stochastic simulations   Ab initio RNA secondary structure predictions have long dismissed helices
interior to loops, so-called pseudoknots, despite their structural importance.
Here, we report that many pseudoknots can be predicted through long time scales
RNA folding simulations, which follow the stochastic closing and opening of
individual RNA helices. The numerical efficacy of these stochastic simulations
relies on an O(n^2) clustering algorithm which computes time averages over a
continously updated set of n reference structures. Applying this exact
stochastic clustering approach, we typically obtain a 5- to 100-fold simulation
speed-up for RNA sequences up to 400 bases, while the effective acceleration
can be as high as 100,000-fold for short multistable molecules (<150 bases). We
performed extensive folding statistics on random and natural RNA sequences, and
found that pseudoknots are unevenly distributed amongst RNAstructures and
account for up to 30% of base pairs in G+C rich RNA sequences (Online RNA
folding kinetics server including pseudoknots : http://kinefold.u-strasbg.fr/
).

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The categories of this paper are: hep-ph
15
The categories of this paper are: nucl-ex
30
The categories of this paper are: q-alg
17
The categories of this paper are: q-fin
8
The categories of this paper are: hep-ex
2
The categories of this paper are: math
12
The categories of this paper are: nucl-th
16
The categories of this paper are: stat
26
The categories of this paper are: bayes-an
37
The categories of this paper are: supr-con
6
The categories of this paper are: astro-ph
1
The categories of this paper are: cs
22
The categories of this paper are: chao-dyn
33
The categories of this paper are: plasm-ph
28
The categories of this paper are: alg-geom
20
The categories of this paper are: acc-phys