iFoldRNA V2.0 – Interactive RNA Folding

iFoldRNA V2.0

:: DESCRIPTION

iFoldRNA is a web portal for interactive RNA folding simulations.

::DEVELOPER

Clemson Computational Biophysics Lab , Dokholyan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iFoldRNA v2: Folding RNA with Constraints.
Krokhotin A, Houlihan K, Dokholyan NV.
Bioinformatics. 2015 Apr 24. pii: btv221

Bioinformatics. 2008 Sep 1;24(17):1951-2. doi: 10.1093/bioinformatics/btn328. Epub 2008 Jun 25.
iFoldRNA: three-dimensional RNA structure prediction and folding.
Sharma S1, Ding F, Dokholyan NV.

TBI – Predicting Ion Effects in RNA Folding

TBI

:: DESCRIPTION

TBI (Tightly Bound Ion Model ) predicts the electrostatic free energy, the different free energy components, the average binding fraction of ions, and the most probable ion binding modes for a given RNA structure (provided in the PDB format) in a salt solution of given ion concentrations.

::DEVELOPER

Shi-Jie Chen Research Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2015 Mar 23;10(3):e0119705. doi: 10.1371/journal.pone.0119705. eCollection 2015.
TBI Server: A Web Server for Predicting Ion Effects in RNA Folding.
Zhu Y, He Z, Chen SJ

BarMap 20080919 – RNA Folding on Dynamic Energy Landscapes

BarMap

:: DESCRIPTION

The program  bar_map  computes a mapping between a series of barrier trees as computed by the barriers program. This of interest in particular in the context of co-transcriptional folding, where the one can compute barrier trees corresponding to different length partial transcripts; or for dynamic landscapes produced e.g. when varying the temperature.

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BarMap

:: MORE INFORMATION

Citation

BarMap: RNA folding on dynamic energy landscapes
Ivo L Hofacker, Christoph Flamm, Christian Heine, Michael T Wolfinger, Gerik Scheuermann, Peter F Stadler
RNA, 2010, 16, 7, 1308-1316

Treekin 0.4 – Computation of RNA Folding Dynamics

Treekin 0.4

:: DESCRIPTION

The program  treekin  computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state.

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Treekin

:: MORE INFORMATION

Citation

Michael T Wolfinger, W Andreas Svrcek-Seiler, Christoph Flamm, Ivo L Hofacker and Peter F Stadler
Efficient computation of RNA folding dynamics
J. Phys. A: Math. Gen. 37 4731,

kinfold 2.2 – Analysis of Time-Resolved RNA Folding

kinfold 2.2

:: DESCRIPTION

kinfold is a software to analyze kinetic progress curves systematically, and then exhaustively enumerate all possible kinetic models to identify the best fitting kinetic model. Local probes of macromolecular structure are measurements that are sensitive to the environment of a relatively small region within a macromolecule. These include, but are not limited to, NMR deuterium exchange and shift perturbation analysis, Fluorescence Resonance Energy Transfer (FRET), and RNA/DNA protein footprinting. The separate transitions reported by individual probes yield unique insight into folding intermediates. While simultaneous acquisition of many unique local transitions provides a cornucopia of information, creating an accurate global description of folding that remains faithful to local details is very challenging.

::DEVELOPER

kinfold Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

 kinfold

:: MORE INFORMATION

Citation:

J.S. Martin, K. Simmons, and A. Laederach.
Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding.
Algorithms. (2009)

fRNAkenstein 20130115 – Python program for Multiple Target Inverse RNA Folding

fRNAkenstein 20130115

:: DESCRIPTION

Frnakenstein is a python program for solving the inverse RNA folding problem, i.e. given a target structure it attempts to design a sequence folding into this stucture.

:: DEVELOPER

James W. J. Anderson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Python

:: DOWNLOAD

 fRNAkenstein

:: MORE INFORMATION

BMC Bioinformatics. 2012 Oct 9;13(1):260.
Frnakenstein: multiple target inverse RNA folding.
Lyngsoe RB, Anderson JW, Sizikova E, Badugu A, Hyland T, Hein J.

Kinwalker – Algorithm for Prediction of RNA Folding Trajectories

Kinwalker

:: DESCRIPTION

The  Kinwalker  algorithm performs cotranscriptional folding of RNAs, starting at a user a specified structure (default: open chain) and ending at the minimum free energy structure. Folding events are performed between transcription of additional bases and are regulated by barrier heights between the source and target structure.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Kinwalker

:: MORE INFORMATION

Citation

J Mol Biol. 2008 May 23;379(1):160-73. Epub 2008 Mar 6.
Folding kinetics of large RNAs.
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C.