Osprey is a tool for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale data sets can be readily combined with Osprey for comparison of different methods.
DockScore is a rigorous scoring scheme which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed.
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.
NAViGaTOR (Network Analysis, Visualization, & Graphing TORonto ) is a software package for visualizing and analyzing protein-protein interaction networks.NAViGaTOR can query OPHID / I2D – online databases of interaction data – and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI).
CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor
3DGarden (Global and Restrained Docking Exploration Nexus) is an integrated software suite for performing protein-protein and protein-polynucleotide docking. For any pair of biomolecules structures specified by the user, 3DGarden’s primary function is to generate an ensemble of putative complexed structures and rank them. The highest-ranking candidates constitute predictions for the structure of the complex. 3DGarden cannot be used to decide whether or not a particular pair of biomolecules interacts. Complexes of protein and nucleic acid chains can also be specified as individual interactors for docking purposes.