Computing folding pathways between RNA secondary structures
نویسندگان
چکیده
منابع مشابه
Computing folding pathways between RNA secondary structures
Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of...
متن کاملExact Folding Dynamics of RNA Secondary Structures
Barrier trees consisting of local minima and their connecting saddle points imply a natural coarse-graining for the description of the energy landscape of RNA secondary structures. Here we show that, based on this approach, it is possible to predict the folding behavior of RNA molecules by numerical integration. Comparison with stochastic folding simulations shows reasonable agreement of the re...
متن کاملComputing Similarity between RNA Structures
The primary structure of a ribonucleic acid (RNA) molecule is a sequence of nucleotides (bases) over the four-letter alphabet {A; C; G; U}. The secondary or tertiary structure of an RNA is a set of base-pairs (nucleotide pairs) which forms bonds between A − U and C − G. For secondary structures, these bonds have been traditionally assumed to be one to one and non-crossing. This paper considers ...
متن کاملThermal folding and mechanical unfolding pathways of protein secondary structures.
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force versus displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession of stretching events, as measured by the order in which contacts are ruptured, is compared to the sequencing of events during thermal folding and unfoldin...
متن کاملA folding algorithm for extended RNA secondary structures
MOTIVATION RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. RESULTS We present a theoretical model capturing both RNA pair families and extended secondary structure motifs ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2009
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkp1054