Zobrazeno 1 - 10
of 232
pro vyhledávání: '"Clote, Peter"'
Autor:
Bayegan, Amir H., Clote, Peter
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structur
Externí odkaz:
http://arxiv.org/abs/1808.03672
Let Sn denote the network of all RNA secondary structures of length n, in which undirected edges exist between structures s, t such that t is obtained from s by the addition, removal or shift of a single base pair. Using context-free grammars, genera
Externí odkaz:
http://arxiv.org/abs/1807.03911
Autor:
Clote, Peter
A network is scale-free if its connectivity density function is proportional to a power-law distribution. Scale-free networks may provide an explanation for the robustness observed in certain physical and biological phenomena, since the presence of a
Externí odkaz:
http://arxiv.org/abs/1807.00215
Autor:
Bayegan, Amir H., Clote, Peter
The Kinfold and KFOLD programs for RNA folding kinetics implement the Gillespie algorithm to generate stochastic folding trajectories from an initial structure s to a target structure t, in which each intermediate secondary structure is obtained from
Externí odkaz:
http://arxiv.org/abs/1802.06328
Autor:
Clote, Peter, Bayegan, Amir H.
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding
Externí odkaz:
http://arxiv.org/abs/1707.03922
Autor:
Garcia-Martin, Juan Antonio, Dotu, Ivan, Fernandez-Chamorro, Javier, Lozano, Gloria, Ramajo, Jorge, Martinez-Salas, Encarnacion, Clote, Peter
Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resou
Externí odkaz:
http://arxiv.org/abs/1605.04468
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first tw
Externí odkaz:
http://arxiv.org/abs/1508.05499
Autor:
Clote, Peter
Given an RNA sequence a, consider the network G = (V;E), where the set V of nodes consists of all secondary structures of a, and whose edge set E consists of all edges connecting two secondary structures whose base pair distance is 1. Define the netw
Externí odkaz:
http://arxiv.org/abs/1508.03815
Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (
Externí odkaz:
http://arxiv.org/abs/1505.04210
Autor:
Senter, Evan, Clote, Peter
In this paper, we introduce the software suite, Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure S of a gi
Externí odkaz:
http://arxiv.org/abs/1501.04648