TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
- Resource Type
- Authors
- Leonardo Pardo; Ivar Lugtenburg; Arnau Cordomí; Mireia Olivella; Xavier Deupi; Eduardo Mayol; Marc Perea
- Source
- BMC Bioinformatics
RIUVic. Repositorio Institucional de la Universidad de Vic
instname
Recercat. Dipósit de la Recerca de Catalunya
- Subject
- Protein Conformation
Amino Acid Motifs
Biology
Bioinformatics
Biochemistry
Database
Sequence motifs
Structural Biology
Sequence Analysis, Protein
Membrane proteins
Extracellular
Humans
Databases, Protein
Gene
Molecular Biology
Internet
Applied Mathematics
Structural gene
Proteïnes de membrana
computer.file_format
Protein Data Bank
Computer Science Applications
Protein Structure, Tertiary
Transmembrane segments
Membrane protein
Structural distortion
Biophysics
Threading (protein sequence)
DNA microarray
Sequence motif
computer
- Language
- English
- ISSN
- 1471-2105
Background Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available crystal structures of these proteins in the Protein Data Bank permits an initial estimation of their structural properties. Description We have developed two web servers—TMalphaDB for α-helix bundles and TMbetaDB for β-barrels—to analyse the growing repertoire of available crystal structures of membrane proteins. TMalphaDB and TMbetaDB permit to search for these specific sequence motifs in a non-redundant structure database of transmembrane segments and quantify structural parameters such as ϕ and ψ backbone dihedral angles, χ 1 side chain torsion angle, unit bend and unit twist. Conclusions The structural information offered by TMalphaDB and TMbetaDB permits to quantify structural distortions induced by specific sequence motifs, and to elucidate their role in the 3D structure. This specific structural information has direct implications in homology modeling of the growing sequences of membrane proteins lacking experimental structure. TMalphaDB and TMbetaDB are freely available at http://lmc.uab.cat/TMalphaDB and http://lmc.uab.cat/TMbetaDB.