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Author: Kevin Keating
Description: RCrane allows for semi-automated building of RNA structure within Coot.
Current version:
0.9 (released October 26, 2011) 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.
Screenshots:
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RCrane.CLI (formerly CONDOR.CLI)
Author: Kevin Keating
Description: RCrane.CLI uses phosphate and glycosidic bond coordinates to predict and build backbone structure. Note that RCrane.CLI is a command line program and is not intended for interactive use. Crystallographers wishing to use this methodology for structure building should use RCrane, above.
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.
Downloading and installation instructions: Please click here to download RCrane.CLI. Instructions for installing and running the program may be found here.
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.
Author:
Carlos Duarte
Description:
AMIGOS reads an RNA PDB file and outputs a complete table of torsion
angle calculations. more
info.
Current version:
0.3 (2003-Aug-30)
Downloading and installation instructions:
AMIGOS is a Perl script - it does not need compilation. Just download
the script from the link below, check to ensure Perl is properly installed on
your machine, and make the file AMIGOS executable. The program is ready
to use. The output of the program is a series of spreadsheets containing conformational
data. If you use KaleidaGraph to view spreadsheet data, the plot template from
the figure above will assist you in viewing the data.
Downloads:
AMIGOS.pl: AMIGOS 0.3
README.txt: README file
template_all.hqx: binhexed Mac KaleidaGraph
plot template
amigos.tar.gz: all the above in one tarred
and gzipped archive.
Author:
Carlos Duarte
Description:
PRIMOS allows the user to perform interactive comparisons between RNA
structures and to conduct database searches for specific RNA structures or substructures. Note that the search capabilities of PRIMOS are also included in AMIGOS II.
Downloading and installation instructions:
Please contact
us if you would like to use PRIMOS. 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.
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.
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.
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