Comments/ Guestbook Home page Dr. Zuker

---

Thermodynamic considerations and rules for RNA folding

• RNA Biophysical Chemistry: The Turner Group at the University of Rochester's Department of Chemistry

• The Turner energy rules for RNA folding. Enthalpies and free energies at arbitrary temperatures.

• The Biocomputing Group at the University of Düsseldorf.

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 T_m prediction.
    • Melting profiles for hetero-dimers.
    • Melting profiles for homo-dimers.
    • Quick "2-state" T_m predictions for multiple pairs of oligos.
  • Download the UNAFold software. OligoArrayAux and mfold_util are also available

  

• The old Zuker-Turner RNA folding package.
  • Contributors
    • Algorithms: Michael Zuker, John Jaeger, David Mathews, Doug Turner
    • Energy rules: Doug Turner, John Jaeger, David Mathews et al.
    • Energy dot plots: Ann Jacobson & Michael Zuker
    • Programing: Michael Zuker and Darrin Stewart
    • RNAstructure, Version 4.6 (5/6/2008)
      A Windows program for the prediction and analysis of RNA secondary structure.
      Author: David H. Mathews, University of Rochester Medical Center.
  • Download mfold and mfold_util software for Unix/Linux computers. Runs on Mac OS X.

  • mfold server. Fold your own sequences on our server.
    • View previous results:   RNA & DNA,   Quikfold

  • efn server:Compute the energy of an RNA or DNA structure.

  • mfold user manual. Update of published version.

  

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

  

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

  

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

  

• 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

• The MC-SYM Package by François Major
  A Computer Science approach to 3D RNA modeling - Solving a CSP (Constraint Satisfaction Problem)

• Professor Stephen C. Harvey at Georgia Tech
  MACROMOLECULAR STRUCTURE AND DYNAMICS
  3D RNA modeling

  

• NDB - The Nucleic Acid Database at Rutgers

  

• The Database of Non-canonical Base Pairs in known RNA structures.
  George E. Fox Lab., University of Houston

• Geometric Classification of Non-Canonical Basepairing in RNA.
  Neocles B. Leontis, Chemistry Dept., Bowling Green State University, OH.

• The RNA Modification Database. Maintained by F. Crain and James A. McCloskey.

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 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 tRNA Sequence Database compiled by Dr. Sprinzl.
  Laboratorium für Biochemie, Bayreuth

• The Poznan RNA Databank of 5S rRNA and 5S rRNA gene sequences.
  Provided by Maciej Symanski.

• The Austin/Halifax Database of
  SSU rRNA, LSU rRNA & group I introns , by
  M. Schnare, M. Gray, S. Damberger & Robin Gutell

  

• The Ribosomal Database Project (RDP)
  Michigan State University

• The European Ribosomal RNA databse at the University of Gent, Belgium

  

• The Ribonuclease P Database

  Maintained by Dr. James (Jim) W. Brown

• The tmRNA Website,   maintained by Kelly Williams.

• Christian Zwieb's databases: University of Texas Health Center at Tyler
  • Signal Reocgnition Particle Database
  • tmRNA Database
  • uRNA Database

  

• Pseudobase - Pseudoknot database maintained by Eke van Batenburg, Theoretical Biology, Leiden University.

• snoRNA Database - Sean Eddy's Lab at Washington University
  Source code for snoscan.

• Larry Simpson's laboratory Web Site, including: his
  • RNA Editing Web Site
  • U-insertion/deletion RNA Editing Web Site and his
  • U-Insertion/Deletion Edited Sequence database.

The RNA World at IMB Jena

• Image Library of Biological Macromolecules

• Software and many other RNA links

Computational RNA Research at the NIH

• Computational Approaches to RNA Structure Analysis
  Bruce A. Shapiro
  1. STRUCTURELAB
  2. RNA Structure Prediction
  3. Visualization Techniques for RNA Secondary Structure
  4. RNA nanobiology

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