Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins

Bioinformatics

Volumn 32, Issue 10, 2016, Pages 1571-1573

  Hayat, Sikander ^a   Peters, Christoph ^b   Shu, Nanjiang ^b,c   Tsirigos, Konstantinos D ^b   Elofsson, Arne ^b  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b SCIENCE FOR LIFE LABORATORY   (Sweden)

^c STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

BIOLOGY; CHEMISTRY; COMPUTER LANGUAGE; MOLECULAR MODEL; PROTEIN SECONDARY STRUCTURE;

COMPUTATIONAL BIOLOGY; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROGRAMMING LANGUAGES; PROTEIN STRUCTURE, SECONDARY;

EID: 84970024921     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw025     Document Type: Article

References (14)

1. Altschul,S. et al. (1997) Gapped blast and psi-blast: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Bagos,P. et al. (2004) PRED-TMBB: A web server for predicting the topology of {beta}-barrel outer membrane proteins. Nucleic Acids Res., 32, W400.
3. Bigelow,H. and Rost,B. (2006) PROFtmb: A web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res., 34, W186.
4. Consortium, U. et al. (2015) Uniprot: A hub for protein information. Nucleic Acids Res., 43, D204.
5. Freeman,T. and Wimley,W. (2010) A highly accurate statistical approach for the prediction of transmembrane b-barrels. Bioinformatics, 26, 1965.
6. Hayat,S. and Elofsson,A. (2012) Boctopus: improved topology prediction of transmembrane b barrel proteins. Bioinformatics, 28, 516-522.
7. Hayat,S. et al. (2015) All-atom 3d structure prediction of transmembrane b-barrel proteins from sequences. Proc. Natl Acad. Sci. USA, 112, 5413-5418.
8. Lomize,M. et al. (2006) OPM: orientations of proteins in membranes database. Bioinformatics, 22, 623-625.
9. Remmert,M. et al. (2009) HHomp-prediction and classification of outer membrane proteins. Nucleic Acids Res., 37, W446.
10. Remmert, M. et al. (2011) Hhblits: lightning-fast iterative protein sequence searching by hmm-hmm alignment. Nat. Methods, 9, 173-175.
11. Rost,B. et al. (1994) Redefining the goals of protein secondary structure prediction. J. Mol. Biol., 235, 13-26.
12. Savojardo,C. et al. (2013) Betaware: A machine-learning tool to detect and predict transmembrane beta barrel proteins in prokaryotes. Bioinformatics, bts728.
13. Wang,G. and Dunbrack,R.L. (2005) Pisces: recent improvements to a pdb sequence culling server. Nucleic Acids Res., 33, W94-W98.
14. Wimley,W. (2003) The versatile b-barrel membrane protein. Curr. Opin. Struct. Biol., 13, 404-411.