期刊
BIOINFORMATICS
卷 32, 期 10, 页码 1571-1573出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btw025
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资金
- Swedish Research Council [VR-NT 2012-5046]
- SSF
- Vinnova through the Vinnova-JSP program
Accurate topology prediction of transmembrane beta-barrels is still an open question. Here, we present BOCTOPUS2, an improved topology prediction method for transmembrane beta-barrels that can also identify the barrel domain, predict the topology and identify the orientation of residues in transmembrane beta-strands. The major novelty of BOCTOPUS2 is the use of the dyad-repeat pattern of lipid and pore facing residues observed in transmembrane beta-barrels. In a cross-validation test on a benchmark set of 42 proteins, BOCTOPUS2 predicts the correct topology in 69% of the proteins, an improvement of more than 10% over the best earlier method (BOCTOPUS) and in addition, it produces significantly fewer erroneous predictions on non-transmembrane beta-barrel proteins.
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