Membrane protein-protein docking data analysis software tools
A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is mainly due to the challenges of crystallizing such proteins or performing NMR spectroscopy analyses. All the more so, there is only a small number of membrane protein-protein complexes with known structure. Therefore, developing computational tools for docking membrane proteins is crucial.
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.
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.
Attempts to customize three docking steps to the lipid bilayer environment. Memdock is an integrated docking algorithm for a-helical membrane proteins which includes the docking, refinement and re-ranking stages designed for docking within the membrane. It performs well and much faster when docking membrane proteins compared with the original algorithms designed for the docking of globular proteins.
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.
Draws on the rich existing functionality of Rosetta3. MPDock is a proof-of-concept application that was adapted for membrane proteins. The protocol consists of two steps: (1) a prepacking step to create a starting structure, and (2) a protein-protein docking in the membrane bilayer. MPDock was tested on five protein-protein complexes in the membrane.
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