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Alpha-helical and beta-sheet membrane- membrane protein dimers: centralizing information
Pedro Matos Filipe * 1 , António José Preto 1 , Panos Koukos 2 , Alexandre Bonvin 2 , Irina Moreira 2, 3
1  Structural, Computational and Chemical Biology, CNC - Center for Neuroscience and Cell Biology, University of Coimbra
2  Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
3  Center for Neurosciences and Cell Biology (CNC.IBILI), Coimbra, Portugal

10.3390/mol2net-03-05107
Abstract:

Bioinformatics allows to automatically characterize a large number of proteins from numerous different databases, thus, uncovering new possible interactions between biomolecules in a huge set of individuals in a conscious and cost-efficient way. Membrane proteins are indisputably important for the assurance of major processes in the cell, occupying approximately 25% of the whole cell genome. In this work, some of the major features displayed at Protein Data Bank (original species, chains and ligands, oligomer state, multimeric states, stoichiometry, among others) of membrane proteins listed in the Membrane Proteins with Known 3D Structure database were registered together using manual and automated methods - some of these methods include the usage of python specific tools (like Selenium and BioPython). We aimed to construct a membrane-membrane dimers database that will serve as input for data-mining algorithms to unveiling new functional and evolutionary knowledge.

Keywords: selenium, biopython, original species, chains and ligands, oligomer state, multimeric states, stoichiometry
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