:: DESCRIPTION
APSSP2 allows to predict the secondary structure of protein’s from their amino acid sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Raghava, G. P. S. (2002)
APSSP2 : A combination method for protein secondary structure prediction based on neural network and example based learning.
CASP5. A-132.
:: DESCRIPTION
RNApdbee is a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
::DEVELOPER
The Bioinformatics Group, Poznan University of Technology.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2014 Apr 25. [Epub ahead of print]
RNApdbee–a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
Antczak M1, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M.
:: DESCRIPTION
RNAmutants is a web server to perform mutational analysis for a given RNA sequence. Previous methods relied on exhaustively enumerating k-point mutant sequences and subsequently applying mfold or RNAfold, a procedure with run time exponential in k. In contrast, RNAmutants computes the minimum free energy structure and Boltzmann partition function for all k-point mutants, for 0 ≤ k ≤ K, with run time O(K2n3).
::DEVELOPER
Clote Lab , Computer Science and Biology at McGill
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
J Comput Biol. 2011 Nov;18(11):1465-79. doi: 10.1089/cmb.2011.0181. Epub 2011 Oct 28.
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.
Waldispühl J1, Ponty Y.
Jerome Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote.
Efficient algorithms for probing the RNA mutation landscape.
PLoS Comput Biol. 2008 Aug 8;4(8):e1000124.
:: DESCRIPTION
Vienna+P is a tool for predicting nucleic acid secondary structure in the presence of single-stranded binding proteins, and implement it as an extension of the Vienna RNA Package.
::DEVELOPER
Ralf Bundschuh’s Statistical Physics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Jan 1;26(1):61-7. doi: 10.1093/bioinformatics/btp627. Epub 2009 Nov 4.
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure.
Forties RA1, Bundschuh R.
:: DESCRIPTION
ALIDOT (ALIgned DOT-plots) detects conserved secondary structure elements in relatively small sets of RNAs by combining multiple sequence alignments and secondary structure predictions. Both a (good) sequence alignment and predicted secondary structure predictions for each sequence in the alignment must be provided as inputs. alidot works either with predicted mfe structures, or with base pairing probability matrices.
The program alidot and the associated perl scripts are part of the Vienna RNA Package.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes
Ivo L. Hofacker and Peter F. Stadler
Comp & Chem., 23, 401-414 (1999)
:: DESCRIPTION
Porter is a server for protein secondary structure prediction based on an ensemble of 25 BRNNs (bidirectional recurrent neural networks)
PaleAle is a server for the prediction of protein relative solvent accessibility.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Aug 15;29(16):2056-8. doi: 10.1093/bioinformatics/btt344. Epub 2013 Jun 14.
Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility.
Mirabello C1, Pollastri G.
:: DESCRIPTION
ScrewFit is an Open Source program for the characterization of protein secondary structures. It provides an efficient description of structural motifs based on simple geometrical assumptions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Biophys Chem. 2009 Apr;141(1):117-23. Epub 2009 Jan 14.
Inhibition of viral group-1 and group-2 neuraminidases by oseltamivir: A comparative structural analysis by the ScrewFit algorithm.
Calligari PA, Kneller GR, Giansanti A, Ascenzi P, Porrello A, Bocedi A.
:: DESCRIPTION
RNAv (RNA secondary structure variation) is a program that searches for RNA secondary structure variations based on the notion of a structure graph to specify the consensus structure of an RNA family.The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.
::DEVELOPER
The RNA-Informatics Research Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Huang, Z., Malmberg, R., Mohebbi M., and Cai, L. (2010)
RNAv: Non-coding RNA Secondary Structure Variation Search via Graph Homomorphism
Proceedings of Computational Systems Bioinformatics Conference (CSB 2010), August, 2010. Vol. 9, p. 56-69.
:: DESCRIPTION
FFTbor computes Boltzmann probability for RNA structural neighbors using the fast Fourier transform.
Given an RNA sequence having metastable secondary structures A,B, the program FFTbor2D computes the ensemble free energy E(x,y)=-RT log Z(x,y), taken over all secondary structures having base pair distance x from A,and base pair distance y from B.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PLoS One. 2012;7(12):e50506. doi: 10.1371/journal.pone.0050506. Epub 2012 Dec 19.
Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
Senter E1, Sheikh S, Dotu I, Ponty Y, Clote P.
J Math Biol. 2015 Jan;70(1-2):173-96. doi: 10.1007/s00285-014-0760-4. Epub 2014 Feb 12.
RNA folding pathways and kinetics using 2D energy landscapes.
Senter E1, Dotu I, Clote P.
:: DESCRIPTION
MSACompro is a novel and practical multiple protein sequence alignment algorithm based on secondary structure, solvent accessibility, and contact map information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 Dec 14;12:472.
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts.
Deng X, Cheng J.