Camps 2.0: Exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins
| Autor: | Angelika Fuchs, Holger Hartmann, Sindy Neumann, Dmitrij Frishman, Antonio J. Martín-Galiano |
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| Rok vydání: | 2011 |
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Molecular Protein Conformation Sequence analysis Computational biology Biology Biochemistry Structural genomics Viral Matrix Proteins Structural bioinformatics Protein structure Sequence Analysis Protein Structural Biology Protein methods Animals Cluster Analysis Humans Databases Protein Molecular Biology Sequence (medicine) Sequence Homology Amino Acid Computational Biology Proteins Markov Chains Protein Structure Tertiary Crystallography Transmembrane domain Membrane protein Viruses Software |
| Zdroj: | Proteins: Structure, Function, and Bioinformatics. 80:839-857 |
| ISSN: | 0887-3585 |
| Popis: | 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/. |
| Databáze: | OpenAIRE |
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