:: DESCRIPTION
meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.
::DEVELOPER
the Institute of Bioinformatics, Innsbruck Medical University
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
meRanTK: methylated RNA analysis ToolKit.
Rieder D, Amort T, Kugler E, Lusser A, Trajanoski Z.
Bioinformatics. 2015 Nov 4. pii: btv647.
:: DESCRIPTION
RNAmigos is a Graph Neural Network for predicting RNA small molecule ligands.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Oliver C, Mallet V, Gendron RS, Reinharz V, Hamilton WL, Moitessier N, Waldispühl J.
Augmented base pairing networks encode RNA-small molecule binding preferences.
Nucleic Acids Res. 2020 Aug 20;48(14):7690-7699. doi: 10.1093/nar/gkaa583. PMID: 32652015; PMCID: PMC7430648.
:: DESCRIPTION
veRNAl is an algorithm for identifying fuzzy recurrent subgraphs in RNA 3D networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Oliver C, Mallet V, Philippopoulos P, Hamilton WL, Waldispühl J.
VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA.
Bioinformatics. 2021 Nov 15:btab768. doi: 10.1093/bioinformatics/btab768. Epub ahead of print. PMID: 34791045.
:: DESCRIPTION
incaRNAfbinv is a web server which implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs.
RNAfbinv is a fragment based RNA design tool. It uses a simulated annealing process to optimize a 2D RNA structure.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Retwitzer MD, Reinharz V, Churkin A, Ponty Y, Waldispühl J, Barash D.
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs.
Bioinformatics. 2020 May 1;36(9):2920-2922. doi: 10.1093/bioinformatics/btaa039. PMID: 31971575.
incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
Drory Retwitzer M, Reinharz V, Ponty Y, Waldispühl J, Barash D.
Nucleic Acids Res. 2016 Jul 8;44(W1):W308-14. doi: 10.1093/nar/gkw440. Epub 2016 May 16.
Bioinformatics. 2013 Nov 15;29(22):2938-40. doi: 10.1093/bioinformatics/btt494. Epub 2013 Aug 23.
RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.
Weinbrand L1, Avihoo A, Barash D.
:: DESCRIPTION
RNA-MoIP is an integer programming framework that refines predicted secondary structures (i.e. removes incorrect canonical base-pairs) to accommodate the insertion of RNA 3D motifs (i.e. hairpins, internal loops and k-way junctions). The predictions can be used as templates to generate complete 3D structures with the MC-Sym program.
::DEVELOPER
Computer Science and Biology at McGill
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yao J, Reinharz V, Major F, Waldispühl J.
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data.
Nucleic Acids Res. 2017 Jul 3;45(W1):W440-W444. doi: 10.1093/nar/gkx429. Erratum in: Nucleic Acids Res. 2017 Jul 3;45(W1):W573. PMID: 28525607; PMCID: PMC5793723.
:: DESCRIPTION
RNAMAP2D is a software to the analysis of contact maps of RNA structures and protein – RNA complexes. The program deals with modified base pairs which are very frequent in RNA and includes ligands and ions which plays key roles in forming and stabilizing RNA structures. What is more, it is possible to show on the computed map whether some of the identified contacts are recognized as belonging to one of the 12 base pairs families, are canonical Watson – Crick pairs, or are 4 classes of stacking interactions. The overlap of the 2D maps of two structures can be easily calculated, providing a measure of RNA structure similarity.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SimRNA is a tool for simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and its applications include RNA 3D structure prediction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM.
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Nucleic Acids Res. 2016 Apr 20;44(7):e63. doi: 10.1093/nar/gkv1479. Epub 2015 Dec 19. PMID: 26687716; PMCID: PMC4838351.
:: DESCRIPTION
ModeRNA is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence via either a fully automated or script-based approaches. ModeRNA is capable of handling 115 different nucleotide modifications and bridging gaps using fragments derived from an extensive fragment library.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Magdalena Rother, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki
ModeRNA: a tool for comparative modeling of RNA 3D structure
Nucl. Acids Res.(2011)doi: 10.1093
:: DESCRIPTION
TSMDA is a novel machine learning method that leverages target and symptom information and negative sample selection to predict miRNA-disease association.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Uthayopas K, de Sá AGC, Alavi A, Pires DEV, Ascher DB.
TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction.
Mol Ther Nucleic Acids. 2021 Aug 26;26:536-546. doi: 10.1016/j.omtn.2021.08.016. PMID: 34631283; PMCID: PMC8479276.
:: DESCRIPTION
EnsembleClust enables fast and accurate clustering of ncRNAs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S48. doi: 10.1186/1471-2105-12-S1-S48.
Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures.
Saito Y1, Sato K, Sakakibara Y.
