software

Go to our archive for older versions

Discrete RNA Libraries from Pseudo-Torsional Space.

Author: Elisabeth Humphris
Description:Libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone.
Reference: Humphris E and Pyle AM. Discrete RNA Libraries from Pseudo-Torsional Space. J Mol Biol,(2012).
Download:RNA Libraries

RCrane

Author: Kevin Keating
Description: RCrane allows for semi-automated building of RNA structure within Coot.
Current version: 1.0 (released April 16, 2012) View changelog
Reference: Keating KS and Pyle AM. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci USA, 107 (2010) 8177-8182.

Video demo:		Screenshots:

Installation instructions: RCrane is now included with nightly builds of Coot, available here. RCrane may be launched via Extensions -> RCrane launch. If you had previously downloaded and installed RCrane and you are running Linux or OS X, please delete ~/.coot-preferences/rcrane.py before using these new versions of Coot with RCrane included. Users of WinCoot do not need to delete anything.
Downloading and installation instructions (Coot 0.6.2 and older): Please click here to download RCrane. Instructions for installing the program may be found here.
Usage instructions: Instructions for using the program may be found here. Additionally, a video demo is available.

AMIGOS II

Author: Leven Wadley
Description: AMIGOS II allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.
Downloading and installation instructions: Please contact us if you would like to use AMIGOS II . You will be required to sign a license agreement, and then we will provide the software and installation instructions by email. It is free for academic use but carries a charge for industrial use.

Qnifft

Description: Qnifft utilizes the non-linear Poisson-Boltzmann (NLPB) equation to calculate the electrostatic potentials of nucleic acids. more info.
Visualizing output: The output of Qnifft can be displayed using Spock or PyMol. For instructions, see the visualization tutorial.

Qnifft 1.4/2.2
Kim Sharp has developed an updated version of Qnifft that can be compiled for both Linux and SGI platforms. This program is available from his website. The Qnifft tutorial is written for version 1.2, but is still helpful for these newer versions.

Qnifft 1.2
Downloading and installation instructions: A binary executable file is available for download. Qnifft has been compiled and tested for Irix 6.2+. For more information, see the tutorial.
Downloads:
Qnifft: the NLPB solver
prm: a sample parameter file
rna2.siz: atomic radii file (from Discover)
rna2.crg: partial atomic charge file (from Discover)
amber.crg: partial atomic charge file (from Amber)
qnifft.tar.gz: all the above files plus the tutorial in one tarred and gzipped archive.

SHEVEK

Author: Phillip S. Pang
Description: SHEVEK predicts long-range tertiary interactions within RNAs, between RNA-protein and protein-protein interactions from sequence alignments.
Reference: "Prediction of Functional Tertiary Interactions and Intermolecular Interfaces From Primary Sequence Data", PS Pang, E Jankowsky, LM Wadley and AM Pyle, J of Experimental Zoology (Mol Dev Evol) (2005), 000, 1-14.
Downloading and installation instructions: Please contact us if you would like to use SHEVEK.

219 Prospect Street Kline Biology Tower, Room 826 Yale University New Haven, CT 06520-8103 Phone: 203-436-4047 (KBT 826)         : 203-432-6370 (KBT 840) FAX: 203-432-5316 Web master Srinivas Somarowthu Last modified:   30-Jan-2013