Vfold 2.0 – RNA Structure and Folding Thermodynamics Prediction

Vfold 2.0

:: DESCRIPTION

Vfold is a software package to evaluate the stable structures and the folding free energies for RNA secondary structures and pseudoknotted structures. Recently, the Vfold model has been extended to predict loop-stem tertiary interactions in RNA pseudoknots

::DEVELOPER

Shi-Jie Chen Research Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 Vfold

:: MORE INFORMATION

Citation

Vfold: a web server for RNA structure and folding thermodynamics prediction.
Xu X, Zhao P, Chen SJ.
PLoS One. 2014 Sep 12;9(9):e107504. doi: 10.1371/journal.pone.0107504. eCollection 2014.

RNA-WL 1.5 – Thermodynamics of RNA structures by Wang-Landau sampling

RNA-WL 1.5

:: DESCRIPTION

RNA-WL is an implementation of the Wang-Landau non-Boltzmannian sampling algorithm to approximate the partition function for RNA secondary structures.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • WebServer
  • C Compiler

:: DOWNLOAD

 RNA-WL

:: MORE INFORMATION

Citation:

Feng Lou, Peter Clote.
Thermodynamics of RNA structures by Wang-Landau sampling.
ISMB 2010, Bioinformatics 2010 Jun 15;26(12):i278-86

OligoWalk 2 – Select Efficient siRNA using Hybridization Thermodynamics

OligoWalk 2

:: DESCRIPTION

OligoWalk is an online sever calculating thermodynamic features of sense-antisense hybidization. It predicts the free energy changes of oligonucleotides binding to a target RNA. It can be used to design efficient siRNA targeting a given mRNA sequence.

::DEVELOPER

Mathews group

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OligoWalk

:: MORE INFORMATION

Citation:

Efficient siRNA selection using hybridization thermodynamics
Zhi John Lu and David H. Mathews
Nucl. Acids Res. (2008) 36 (2): 640-647

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