WCOACH

WCOACH is a graph clustering algorithm to detect protein complexes in weighted Protein-Protein Interaction (PPI) networks. protein complexe prediction is a chalanging problem in computational biology. WCOACH algorithm is a modification of COACH method to solve this problem in weighted PPI networks.

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RNASHAPE

RNA molecules play important and fundamental roles in biological processes. Frequently, the functional form of single-stranded RNA molecules requires a specific tertiary structure. Classically, RNA structure determination has mostly been accomplished by X-Ray crystallography or Nuclear Magnetic Resonance approaches. These experimental methods are time consuming and expensive. In the past two decades, some computational methods and algorithms have been developed for RNA secondary structure prediction. In these algorithms, minimum free energy is known as the best criterion. However, the results of algorithms show that minimum free energy is not a sufficient criterion to predict RNA secondary structure. These algorithms need some additional knowledge about the structure, which has to be added in the methods. Recently, the information obtained from some experimental data, called SHAPE, can greatly improve the consistency between the native and predicted RNA secondary structure.

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ESD-Fold

ESD-Fold is a new method to predict RNA secondary structure based on both minimum free energy and SHAPE- directed pseudo-free energy. For each RNA sequence, this method employs a base pair probability matrix of all potential stems to construct a population of RNA secondary structures. It should be noted that RNAfold software, that is free of charge for academic users and available in address "http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi", is applied to compute the matrix. Then, for each constructed secondary structure, its SHAPE data is simulated. After that, an evolutionary algorithm is used to improve each structure based on both free and pseudo-free energies. Population generation is continued until the best individual in the two last populations remains fixed. Then, a structure with minimum summation of free energy and pseudo-free energy is considered as the predicted RNA secondary structure.

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GRNAs

The GRNAs predicts RNA-RNA interaction structures including kissing hairpins. GRNAs computes the minimum free energy (MFE) structures by using a novel genetic algorithm

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GAPSSIF

GAPSSIF is a novel genetic algorithm which uses native secondary sub-structures is proposed to solve Protein Secondary Structure Inverse Folding (PSSIF) problem. In essence, evolutionary information can lead the algorithm to design appropriate amino acid sequences respective to the target secondary structures. Furthermore, they can be folded to tertiary structures almost similar to their reference 3D structures.

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HRDSSD

HRDSSD is a new method for accurate design of RNA sequences based on their secondary structures using SHAPE data as pseudo-free energy. We first use a stochastic model to simulate SHAPE data based on a set of 16S and 23S ribosomal RNA sequences. Then, a harmony search algorithm is applied to accurately predict RNA sequence using free energy and simulated SHAPE data.

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