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Camps 2.0: Exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins
Proteins, structure, function, and bioinformatics, 2012-03, Vol.80 (3), p.839-857
Neumann, Sindy
Hartmann, Holger
Martin-Galiano, Antonio J.
Fuchs, Angelika
Frishman, Dmitrij
2012
Volltextzugriff (PDF)
Details
Autor(en) / Beteiligte
Neumann, Sindy
Hartmann, Holger
Martin-Galiano, Antonio J.
Fuchs, Angelika
Frishman, Dmitrij
Titel
Camps 2.0: Exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins
Ist Teil von
Proteins, structure, function, and bioinformatics, 2012-03, Vol.80 (3), p.839-857
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2012
Quelle
MEDLINE
Beschreibungen/Notizen
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.
Sprache
Englisch
Identifikatoren
ISSN: 0887-3585
eISSN: 1097-0134
DOI: 10.1002/prot.23242
Titel-ID: cdi_proquest_miscellaneous_921146049
Format
–
Schlagworte
Animals
,
Cluster Analysis
,
clustering
,
Computational Biology - methods
,
Databases, Protein
,
evolution
,
hidden Markov models
,
Humans
,
Markov Chains
,
Models, Molecular
,
Protein Conformation
,
Protein Structure, Tertiary
,
Proteins - chemistry
,
Sequence Analysis, Protein - methods
,
sequence comparison
,
Sequence Homology, Amino Acid
,
Software
,
structural genomics
,
structure classification
,
Viral Matrix Proteins - chemistry
,
Viruses - chemistry
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