Tag: Folding Pathway

RNAEAPath 1.0 – Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks

RNAEAPath 1.0

:: DESCRIPTION

RNAEAPath provides an alternate approach for predicting low-barrier folding pathways between RNA conformational secondary structures.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAEAPath

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S5. doi: 10.1186/1471-2105-13-S3-S5.
Predicting folding pathways between RNA conformational structures guided by RNA stacks.
Li Y, Zhang S.

RNApathfinder – Analyze Near-optimal Folding Pathways between RNA Secondary Structures

RNApathfinder

:: DESCRIPTION

RNApathfinder is a web server to compute near-optimal folding pathways between two given secondary structures for a given RNA sequence. Since this problem is known to be NP-complete, our main algorithm, RNAtabupath uses the TABU local search heuristic. The web server includes both downloadable source code for several algorithms, as well as a web engine to compute pathways. Intended applications concern folding pathways for RNA conformational switches.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • WebServer
  • Python

:: DOWNLOAD

 RNApathfinder

:: MORE INFORMATION

Citation:

I. Dotú, W.A. Lorenz, P. Van Hentenryck, P. Clote.
Computing folding pathways between RNA secondary structures.
Nucleic Acids Res. 2010 Mar 1;38(5):1711-22.