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DOCK/PIERR
Predicts structures of transmembrane protein complexes. DOCK/PIERR is a docking algorithm that predicts, in atomic resolution, the structure of the complex formed by two proteins, given their individual tertiary structure. The conformational space of complexes is sampled exhaustively using Fast Fourier Transforms. The software uses the potentials Protein Interaction Energy (PIE) and Protein Interfaces, Surfaces and Assemblies (PISA) for scoring residue and atomic contacts at protein interfaces.
CoPIT / co-interacting protein identification technology
Allows comprehensive identification and analysis of membrane protein interactomes and their dynamics. CoPIT integrates experimental and computational methods for a coimmunoprecipitation (Co-IP)-based workflow from sample preparation for mass spectrometric analysis to visualization of protein-protein interaction networks. The approach particularly improves the results for membrane protein interactomes, which have proven to be difficult to identify and analyze.
MBPpred
A profile hidden Markov model based method capable of detecting membrane binding proteins (MBPs) from information encoded in their amino acid sequence. MBPpred identifies MBPs that contain one or more of the membrane binding domains (MBDs) that have been described to date, and further classifies these proteins based on their position in respect to the membrane, either as peripheral or transmembrane. This method was applied in selected eukaryotic proteomes, in order to examine the characteristics they exhibit in various eukaryotic kingdoms and phyla.
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