TMBpro: secondary structure, β-contact and tertiary structure prediction of transmembrane β-barrel proteins. Motivation: Transmembrane β-barrel (TMB) proteins are embedded in the outer membranes of mitochondria, Gram-negative bacteria and chloroplasts. These proteins perform critical functions, including active ion-transport and passive nutrient intake. Therefore, there is a need for accurate prediction of secondary and tertiary structure of TMB proteins. Traditional homology modeling methods, however, fail on most TMB proteins since very few non-homologous TMB structures have been determined. Yet, because TMB structures conform to specific construction rules that restrict the conformational space drastically, it should be possible for methods that do not depend on target-template homology to be applied successfully. Availability:

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  1. Tran, Van Du T.; Chassignet, Philippe; Steyaert, Jean-Marc: On permuted super-secondary structures of transmembrane (\beta)-barrel proteins (2014)
  2. Wang, Han; Liu, Bo; Sun, Pingping; Ma, Zhiqiang: A topology structure based outer membrane proteins segment alignment method (2013) ioport
  3. Hayat, Sikander; Park, Yungki; Helms, Volkhard: Statistical analysis and exposure status classification of transmembrane beta barrel residues (2011)
  4. Stelle, Diogo; Barioni, Maria C.; Scott, Luis P.: Using data mining to identify structural rules in proteins (2011)
  5. Randall, Arlo Z.; Cheng, Jianlin; Sweredoski, Michael J.; Baldi, Pierre: Tmbpro: Secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. (2008) ioport