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*Thermodynamic considerations and rules for RNA folding


* RNA folding and search software

  • The UNAFold package: Prediction of hybridization, folding and melting profiles. N.R. Markham & M. Zuker.
    Auxilliaray mfold_util package for for creating structure and dot plots.
    • Contributors
      • Algorithms: Roumen Dimitrov, Nick Markham & Michael Zuker
      • Software:
        • UNAFold:   Nick Markham
        • mfold_util:   Darrin Stewart & Michael Zuker; (porting and revisions by Nick Markham, Alex Yu and Michael Zuker)
        • DINAMelt web server:  Nick Markham; equipment donated by IBM Research
      • Energy rules for RNA: Doug Turner, David Mathews et al.
      • Energy rules for DNA: John SantaLucia et al.
    • The DINAMelt web server for melting profile and Tm prediction.
    • Download the UNAFold software. OligoArrayAux and mfold_util are also available

    mfold Icon

  • The old Zuker-Turner RNA folding package.

    HMMER Logo

  • HMMER, Infernal and more: Software from the lab of Sean Eddy, HHMI, Janelia Farm Research Campus.

    Austrian Flag

  • The famous Vienna RNA software package, by Ivo Hofacker, Institut für theoretische Chemie, Vienna.

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  • The WWW: RNA secondary structure prediction server at the Belozersky Institute of physico-chemical biology at Moscow State University.

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  • The ESSA package from the Département de Biométrie et Intelligence Artificielle, INRA.

  • RNAdraw - by Ole Matzura (see below)

  • Bruce Shapiro's STRUCTURELAB at the NIH.
    (see below)

* 3D RNA modeling & databases


* RNA secondary structure display software

  • sir_graph:
    An interactive program by Darrin Stewart and Michael Zuker
    for Unix/Linux computers (includes Mac OS X).
    Part of the mfold_util software package.


  • XRNA:
    High quality images/interactive program
    By: Bryn Weiser and Harry Noller at UC Santa Cruz.

    RNA Moview

  • RNA Movies: Visualising RNA Secondary Structure Spaces.
    Created by the Technische Fakultät group at University of Bielefeld.

  • SStructView: RNA Secondary Structure Java Applet
    from the Helix Group at Stanford University.

  • RnaViz: A windows-type program for producing secondary structure drawings of RNA molecules.
    by Peter De Rijk and Rupert De Wachter

  • The Rnadraw Homepage (from Sweden). Author is Ole Matzura

* Secondary Structures & Databases


* The RNA World at IMB Jena

  • Image Library of Biological Macromolecules

  • Software and many other RNA links

* Computational RNA Research at the NIH


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RPI Logo Michael Zuker
Rensselaer Polytechnic Institute
Created: 10/6/95
Last Update: 5/19/08