:: DESCRIPTION
PSpro is a software to predict secondary structure, solvent accessibility, and residue-residue contacts . It is essentially a bundle of three tools including SSpro 4.1, ACCpro 4.1 and NNcon 1.0.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
RNAmute is an application that provides a user friendly interface for analyzing the effects of point mutations on RNAs secondary structure.
XRNAmute is RNAmute web server for the mutational analysis of RNA secondary structures.
::DEVELOPER
A.Churkin and D. Barash (dbarash@cs.bgu.ac.il)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W92-9. doi: 10.1093/nar/gkr207. Epub 2011 Apr 7.
The RNAmute web server for the mutational analysis of RNA secondary structures.
Churkin A1, Gabdank I, Barash D.
A.Churkin and D. Barash,
“RNAMute: RNA Secondary Structure Mutation Analysis Tool,”
BMC Bioinformatics, 7:221, 2006.
:: DESCRIPTION
SIMPA (SIMilar Peptide Analysis) is a program for predicting the secondary structure of proteins. 3 states are taken into consideration: alpha helix (H), beta strand (b) and aperiodical structures (C). This program is based on the nearest neighbour notion. It provides a Q3 result of 67%
::DEVELOPER
Jonathan Levin jon@glycine.jouy.inra.fr
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Levin JM, Pascarella S, Argos P, Garnier J.
Quantification of secondary structure prediction improvement using multiple alignments. (1993)
Protein Eng. 6:849-54.
:: DESCRIPTION
RNAentropy implements two cubic time algorithms to compute the RNA thermodynamic structural entropy.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
RNA Thermodynamic Structural Entropy.
Garcia-Martin JA, Clote P.
PLoS One. 2015 Nov 10;10(11):e0137859. doi: 10.1371/journal.pone.0137859.
:: DESCRIPTION
VARNA (Viral Associated RNAs) is Java lightweight Applet dedicated to drawing the secondary structure of RNA. It is also a Swing component that can be very easily included in an existing Java code working with RNA secondary structure to provide a fast and interactive visualization.Being free of fancy external library dependency and/or network access, the VARNA Applet can be used as a base for a standalone applet. It looks reasonably good and scales up or down nicely to adapt to the space available on a web page, thanks to the anti-aliasing drawing primitives of Swing.
::DEVELOPER
Created by: Kevin Darty, Alain Denise and Yann Ponty ( ponty@lri.fr)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
VARNA: Interactive drawing and editing of the RNA secondary structure
Kévin Darty, Alain Denise and Yann Ponty
Bioinformatics, pp. 1974-1975, Vol. 25, no. 15, 2009
:: DESCRIPTION
RNABOB is an implementation of D. Gautheret’s RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules. (Computer scientists would probably cringe in horror. It works, and it’s fast, but is it street legal in a computer science department? Who knows.) An RNABOB motif is a consensus pattern a la PROSITE patterns, but with base-pairing.
::DEVELOPER
Sean Eddy, Eddy lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
NIAS is a server to help the analysis of the conformational preferences of amino acid residues in proteins.
::DEVELOPER
SBCB – Structural Bioinformatics and Computational Biology Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Borguesan, B.; Inostroza-Ponta, M.; Dorn, M.
NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.
Journal of Computational Biology. March 2017, 24(3): 255-265.
:: DESCRIPTION
forna is a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
forna (force-directed RNA): Simple and Effective Online RNA Secondary Structure Diagrams.
Kerpedjiev P, Hammer S, Hofacker IL.
Bioinformatics. 2015 Jun 22. pii: btv372.
:: DESCRIPTION
RME predict RNA secondary structure by integrating the free energy model with probing data (SHAPE, PARS, DMS).
::DEVELOPER
Lu Lab, School of Life Sciences, Tsinghua University, China
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2015 Sep 3;43(15):7247-59. doi: 10.1093/nar/gkv706. Epub 2015 Jul 13.
Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.
Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, Yang ZR, Mathews DH, Lu ZJ
:: DESCRIPTION
RNAex is an RNA secondary structure prediction enhanced by high-throughput experimental data
::DEVELOPER
Lu Lab, School of Life Sciences, Tsinghua University, China
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.
Wu Y, Qu R, Huang Y, Shi B, Liu M, Li Y, Lu ZJ.
Nucleic Acids Res. 2016 May 2. pii: gkw362.