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Ranking models of t...
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Hayat, SikanderStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
(författare)
Ranking models of transmembrane beta-barrel proteins using Z-coordinate predictions
- Artikel/kapitelEngelska2012
Förlag, utgivningsår, omfång ...
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2012-06-09
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Oxford University Press (OUP),2012
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electronicrdacarrier
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LIBRIS-ID:oai:DiVA.org:su-80010
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https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-80010URI
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https://doi.org/10.1093/bioinformatics/bts233DOI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:ref swepub-contenttype
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Ämneskategori:art swepub-publicationtype
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AuthorCount:2;
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Motivation: Transmembrane beta-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few beta-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful. Results: Here, we present tobmodel; a method for generating 3D models of beta-barrel transmembrane proteins. First, alternative topologies are obtained from the BOCTOPUS topology predictor. Thereafter, several 3D models are constructed by using different angles of the beta-sheets. Finally, the best model is selected based on agreement with a novel predictor, ZPRED3, which predicts the distance from the center of the membrane for each residue, i.e. the Z-coordinate. The Z-coordinate prediction has an average error of 1.61 A. Tobmodel predicts the correct topology for 75% of the proteins in the dataset which is a slight improvement over BOCTOPUS alone. More importantly, however, tobmodel provides a C alpha template with an average RMSD of 7.24 A from the native structure.
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Elofsson, ArneStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)(Swepub:su)aelof
(författare)
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Stockholms universitetInstitutionen för biokemi och biofysik
(creator_code:org_t)
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Ingår i:Bioinformatics: Oxford University Press (OUP)28:12, s. i90-I961367-48031367-4811
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