37 citations · 123 across the 13 of their papers we have counts for
9 papers · 1 filter
Small-world networks and RNA secondary structures
Defne Surujon, Yann Ponty, Peter Clote
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, remov…
RNA folding kinetics using Monte Carlo and Gillespie algorithms?
Peter Clote, Amir H. Bayegan
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 p…
RNAiFold2T: Constraint Programming design of thermo-IRES switches
Juan Antonio Garcia-Martin, Ivan Dotu, Javier Fernandez-Chamorro +4
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 shoc…
RNA thermodynamic structural entropy
Juan Antonio Garcia-Martin, Peter Clote
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation…
Asymptotic connectivity for the network of RNA secondary structures
Peter Clote
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 t…
RNAiFold 2.0: A web server and software to design custom and Rfam-based RNA molecules
Juan Antonio Garcia-Martin, Ivan Dotu, Peter Clote
Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAi…
Fast, approximate kinetics of RNA folding
Evan Senter, Peter Clote
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…
Expected degree for RNA secondary structure networks
Peter Clote
Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degr…
Complete RNA inverse folding: computational design of functional hammerhead ribozymes
Ivan Dotu, Juan Antonio Garcia-Martin, Betty L. Slinger +3
Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st centur…