:: DESCRIPTION
ParaRNAis a software for computing parametric alignment of two RNA structures. It takes two RNA secondary structures and match score, indel score, the range of mismatch score and the range of gap score as its input, and computes all the optimal alignments in the parametric space given by mismatch score and gap score, and show them in a graphic interface.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations.
::DEVELOPER
:: SCREENSHOTS
N/a
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.
Kumar R, Grubmüller H.
Bioinformatics. 2015 Apr 2. pii: btv190.
:: DESCRIPTION
ernwin is a program for sampling coarse grain 3D RNA structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Predicting RNA 3D structure using a coarse-grain helix-centered model.
Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL.
RNA. 2015 Jun;21(6):1110-21. doi: 10.1261/rna.047522.114.
:: DESCRIPTION
RSmatch is a package for comparing RNA structures via 1) pair-wise and DB searches; 2) multiple structure alignment with common structure computation; 3)iterative DB searches.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA.
RADAR: a web server for RNA data analysis and research.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W300-4. doi: 10.1093/nar/gkm253. Epub 2007 May 21. PMID: 17517784; PMCID: PMC1933136.
:: DESCRIPTION
Vfold is a software package to evaluate the stable structures and the folding free energies for RNA secondary structures and pseudoknotted structures. Recently, the Vfold model has been extended to predict loop-stem tertiary interactions in RNA pseudoknots
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Vfold: a web server for RNA structure and folding thermodynamics prediction.
Xu X, Zhao P, Chen SJ.
PLoS One. 2014 Sep 12;9(9):e107504. doi: 10.1371/journal.pone.0107504. eCollection 2014.
:: DESCRIPTION
PRI-Modeler (protein-RNA interaction modeler)analyzes the conformation of the RNA, calculates the hydrogen bond (H bond) and van der Waals interactions between amino acids and nucleotides, extracts secondary and tertiary RNA structure elements, and identifies the patterns of interactions between the proteins and RNAs. This paper presents PRI-Modeler and its application to the hydrogen bond and van der Waals interactions in the most representative set of protein-RNA complexes. The analysis reveals several interesting interaction patterns at various levels.
::DEVELOPER
Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kyungsook Han, Chirag Nepa
PRI-Modeler: Extracting RNA structural elements from PDB files of protein–RNA complexes
FEBS Lett. 2007 May 1;581(9):1881-90.
:: DESCRIPTION
Gardenia is a program that Compares & aligns RNA secondary structures,without pseudoknots. The resulting alignment takes into account both the primary structure and the secondary structure.
::DEVELOPER
Bonsai Bioinformatics – INRIA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet
Alignment of RNA structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008
:: DESCRIPTION
RNAsnp is a software for efficient detection of local RNA secondary structure changes induced by SNPs
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hum Mutat. 2013 Apr;34(4):546-56. doi: 10.1002/humu.22273.
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.
:: DESCRIPTION
SAVoR is an easy-to-use web application that allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SAVoR: a server for sequencing annotation and visualization of RNA structures.
Li F, Ryvkin P, Childress DM, Valladares O, Gregory BD, Wang LS.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W59-64. doi: 10.1093/nar/gks310.
