TMalphaDB contains 430 structures of α-helix bundles. For a full list of proteins click
here.
To avoid redundancy, only one structure for each protein is selected according to resolution and resemblance to the native state. Each structure is characterized by the PDB identification code, protein name, Uniprot accession code, family name (according to OPM1) and organism.
TMbetaDB server is also available for beta-barrel TM proteins.
The project is leaded by Mireia Olivella
and currently maintained by Eduardo Mayol
Interactions
Inter-residue interactions of this dataset have been analyzed in "Inter-residue interactions in alpha-helical transmembrane proteins" Mayol, E. et al (Bioinformatics 2018)
Tables and values can be downloaded from here
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GLOB set bundles
GLOB set complete pdbs
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References
1Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625
2 Blondelle SE, Forood B, Houghten RA, Pérez-Payá. Secondary structure induction in aqueous vs membrane-like environments. Biopolymers, 1997. 42(4): 489-98.
3 Tusnády GE, Dosztányi Z, Simon I. TMDET: web server for detecting transmembrane regions of proteins by using 3D coordinates. Bioinformatics. 2005, 21(7):1276-7.
4 Bansal M, Kumar S, Velavan R (2000) HELANAL: a program to characterize helix geometry in proteins.J Biomol Struct Dyn. 2000 Apr;17(5):811-9.
5 Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T., & Sussman, J. L. (2013). JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry.
Last update: February 2017.
Last modified: October 2018.
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