MTide is an integrated tool for the identification of miRNA-target interaction in plants. The core algorithm consists of a modified miRDeep2 and a modified CleaveLand4.
Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.
Hi-Jack, a novel computational framework, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking.
Genes2Networks (G2N) is a tool that can be used to place lists of mammalian genes in the context of a background mammalian signalome and interactome networks. The input to the program is a list of human Entrez Gene gene symbols and background networks in SIG format, while the output includes: (a) all identified interactions for the genes/proteins, (b) a subnetwork connecting the genes/proteins using intermediate components that are used to connect the genes, (c) ranking of the specificity of intermediate components to interact with the list of genes/proteins.
iPPI-Esml is an ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC.
The web-server PPI is used to predict the protein-protein interaction.The protein sequence are represented by chaos game representation and wavelets transform. The chaos game representation encodes the amino acid position of the proteion and then two discrete series are gotten. The wavelets transform is used to analyse the two series. Finally the random forests algorithm is used for PPIs prediction.
The web-server PPI_RF is used to predict the protein-protein interaction. Based on the physicochemical descriptors, a protein could be converted into several digital signals and then wavelet transform was used to analyze them. With such a formulation frame to represent the samples of protein sequences, the random forests algorithm was adopted to conduct prediction.