Structure Prediction, Visualization, and Design

Contains links to applications for the visualization, prediction, and design of RNA molecules including siRNAs, secondary structure, and folding kinetics.

Found 79 links

Displaying 79 links

TitleTypeCitation CountURL
ARTS
60
http://bioinfo3d.cs.tau.ac.il/ARTS/
AsiDesigner
7
http://sysbio.kribb.re.kr/AsiDesigner/
CARNA
0
http://rna.informatik.uni-freiburg.de/CARNA
CARNAC
130
http://bioinfo.lifl.fr/carnac
CentroidFold
30
http://www.ncrna.org/centroidfold/
CentroidHomfold-LAST
2
http://www.ncrna.org/centroidhomfold/
CorreLogo
19
http://correlogo.abcc.ncifcrf.gov/
CyloFold
9
http://cylofold.abcc.ncifcrf.gov/
DEQOR
106
http://deqor.mpi-cbg.de/deqor_new/input.html
DIAL
28
http://bioinformatics.bc.edu/clotelab/DIAL/
DINAMelt
944
http://mfold.rna.albany.edu/?q=DINAMelt
E-RNAi
579
http://e-rnai.dkfz.de/
ERPIN
165
http://tagc.univ-mrs.fr/erpin/
FASTR3D
5
http://genome.cs.nthu.edu.tw/FASTR3D/
FOLDALIGN
155
http://foldalign.ku.dk
IDT SciTools
22
http://www.idtdna.com/SciTools/SciTools.aspx
ILM
383
http://cic.cs.wustl.edu/RNA/
INFO-RNA
42
http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/start.html
ITS2
276
http://its2.bioapps.biozentrum.uni-wuerzburg.de/
K2N
20
http://www.ibi.vu.nl/programs/k2nwww/
Kinefold
83
http://kinefold.u-strasbg.fr/
KOSMOS
N/A
http://bioengineering.skku.ac.kr/kosmos
LNAtools
75
http://www.exiqon.com/oligo-tools
LocalMove
4
http://bioinformatics.bc.edu/clotelab/localmove/
Mfold
5095
http://mfold.rna.albany.edu/?q=mfold/download-mfold
MolMovDB
136
http://molmovdb.org/
MolProbity
2881
http://molprobity.biochem.duke.edu/
MoViES
15
http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl
NAFlex
N/A
http://www.mmb.irbbarcelona.org/NAFlex
NAPP
1
http://napp.u-psud.fr/
NDB Tools
1276
http://ndbserver.rutgers.edu/services/
NOBAI
29
http://www.manet.uiuc.edu/nobai/nobai.php
NONCODE
1
http://www.noncode.org
OligoWalk
14
http://rna.urmc.rochester.edu/servers/oligowalk
PETfold & PETcofold
3
http://rth.dk/resources/petfold/
Pfold
560
http://www.daimi.au.dk/~compbio/pfold
PKNOTS
546
ftp://selab.janelia.org/pub/software/pknots/
pknotsRG
240
http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/
PSEUDOVIEWER
139
http://pseudoviewer.inha.ac.kr/
psRobot
N/A
http://omicslab.genetics.ac.cn/psRobot/
QGRS Mapper
62
http://bioinformatics.ramapo.edu/QGRS/index.php
QuadFinder
29
http://miracle.igib.res.in/quadfinder/
R3D Align
N/A
http://rna.bgsu.edu/r3dalign/
R3D-BLAST
1
http://genome.cs.nthu.edu.tw/R3D-BLAST/
RADAR
68
http://datalab.njit.edu/biodata/rna/RSmatch/server.htm
RNA Analyzer
28
http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/
RNA Movies
36
http://bibiserv.techfak.uni-bielefeld.de/rnamovies/
RNA Studio
22
http://bibiserv.techfak.uni-bielefeld.de/bibi/Tools_RNA_Studio.html
RNAbor
4
http://bioinformatics.bc.edu/clotelab/RNAbor/
RNAfold
39
http://www.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
RNAiFold
N/A
http://bioinformatics.bc.edu/clotelab/RNAiFold
RNALogo
18
http://rnalogo.mbc.nctu.edu.tw/
RNALOSS
13
http://bioinformatics.bc.edu/clotelab/RNALOSS/
RNAmutants
5
http://bioinformatics.bc.edu/clotelab/RNAmutants/
RNAmute
4
http://www.cs.bgu.ac.il/~xrnamute/XRNAmute
RNAsnp
N/A
http://rth.dk/resources/rnasnp/
RNAsoft
155
http://www.rnasoft.ca/
RNAstructure
N/A
http://rna.urmc.rochester.edu/RNAstructureWeb
RNAtips
N/A
http://rnatips.org
RNAz
950
http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi
Rtips
N/A
http://rna.naist.jp/
SARA
14
http://sgu.bioinfo.cipf.es/services/SARA/
SAVoR
N/A
http://tesla.pcbi.upenn.edu/savor
SEM
4
http://dicsoft2.physics.iisc.ernet.in/sem/
SETTER
N/A
http://siret.cz/setter
Sfold
637
http://sfold.wadsworth.org
siDirect
738
http://design.RNAi.jp/
siRNA Selection Server
215
http://jura.wi.mit.edu/bioc/siRNA
siRNAdb
N/A
http://sirna.cgb.ki.se/
siVirus
17
http://sivirus.rnai.jp/
SPARCS
N/A
http://csb.cs.mcgill.ca/nasp
SStructView
18
http://helix-web.stanford.edu/sstructview/home.html
taveRNA
64
http://compbio.cs.sfu.ca/taverna/
TROD
326
http://www.cellbio.unige.ch/RNAi.html
Vienna RNA Package
945
http://www.tbi.univie.ac.at/~ivo/RNA/
Vienna RNA Websuite
215
http://rna.tbi.univie.ac.at/
WAR
16
http://genome.ku.dk/resources/war
WebFEATURE
121
http://feature.stanford.edu/webfeature/
WebFR3D
0
http://rna.bgsu.edu/webfr3d

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