Research Article
Camps 2.0: Exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins
Sindy Neumann,
Holger Hartmann,
Antonio J. Martin-Galiano,
Angelika Fuchs,
Dmitrij Frishman,
Sindy Neumann
Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
Search for more papers by this authorHolger Hartmann
Gene Center and Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
Search for more papers by this authorAntonio J. Martin-Galiano
Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
Search for more papers by this authorAngelika Fuchs
pRED, Pharma Research and Early Development, pRED Informatics, Roche Diagnostics GmbH, 82377 Penzberg, Germany
Search for more papers by this authorCorresponding Author
Dmitrij Frishman
Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
Department of Genome Oriented Bioinformatics, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany===Search for more papers by this authorSindy Neumann,
Holger Hartmann,
Antonio J. Martin-Galiano,
Angelika Fuchs,
Dmitrij Frishman,
Sindy Neumann
Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
Search for more papers by this authorHolger Hartmann
Gene Center and Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
Search for more papers by this authorAntonio J. Martin-Galiano
Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
Search for more papers by this authorAngelika Fuchs
pRED, Pharma Research and Early Development, pRED Informatics, Roche Diagnostics GmbH, 82377 Penzberg, Germany
Search for more papers by this authorCorresponding Author
Dmitrij Frishman
Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
Department of Genome Oriented Bioinformatics, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany===Search for more papers by this authorAbstract
Structural bioinformatics of membrane proteins is still in its infancy, and the picture of their fold space is only beginning to emerge. Because only a handful of three-dimensional structures are available, sequence comparison and structure prediction remain the main tools for investigating sequence–structure relationships in membrane protein families. Here we present a comprehensive analysis of the structural families corresponding to α-helical membrane proteins with at least three transmembrane helices. The new version of our CAMPS database (CAMPS 2.0) covers nearly 1300 eukaryotic, prokaryotic, and viral genomes. Using an advanced classification procedure, which is based on high-order hidden Markov models and considers both sequence similarity as well as the number of transmembrane helices and loop lengths, we identified 1353 structurally homogeneous clusters roughly corresponding to membrane protein folds. Only 53 clusters are associated with experimentally determined three-dimensional structures, and for these clusters CAMPS is in reasonable agreement with structure-based classification approaches such as SCOP and CATH. We therefore estimate that ∼1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at http://webclu.bio.wzw.tum.de/CAMPS2.0/. Proteins 2011. © 2012 Wiley Periodicals, Inc.
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