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.
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).
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.
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.
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.
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.
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.
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.
MSACompro is a novel and practical multiple protein sequence alignment algorithm based on secondary structure, solvent accessibility, and contact map information.