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Items: 1 to 20 of 207

1.

More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology.

Wong WC, Maurer-Stroh S, Eisenhaber F.

PLoS Comput Biol. 2010 Jul 29;6(7):e1000867. doi: 10.1371/journal.pcbi.1000867.

2.

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins.

Wong WC, Maurer-Stroh S, Eisenhaber F.

Biol Direct. 2011 Oct 25;6:57. doi: 10.1186/1745-6150-6-57.

3.

Accurate domain identification with structure-anchored hidden Markov models, saHMMs.

Tångrot JE, Kågström B, Sauer UH.

Proteins. 2009 Aug 1;76(2):343-52. doi: 10.1002/prot.22349.

PMID:
19173309
5.

ProFAT: a web-based tool for the functional annotation of protein sequences.

Bradshaw CR, Surendranath V, Habermann B.

BMC Bioinformatics. 2006 Oct 23;7:466.

6.

AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings.

Gewehr JE, Hintermair V, Zimmer R.

Bioinformatics. 2007 May 15;23(10):1203-10. Epub 2007 Mar 22.

PMID:
17379694
8.

Recent improvements to the SMART domain-based sequence annotation resource.

Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P.

Nucleic Acids Res. 2002 Jan 1;30(1):242-4.

9.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

PMID:
12386002
10.

dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity.

Wong WC, Yap CK, Eisenhaber B, Eisenhaber F.

Biol Direct. 2015 Aug 1;10:39. doi: 10.1186/s13062-015-0068-3.

11.

EVEREST: automatic identification and classification of protein domains in all protein sequences.

Portugaly E, Harel A, Linial N, Linial M.

BMC Bioinformatics. 2006 Jun 2;7:277.

13.

Protein domain identification and improved sequence similarity searching using PSI-BLAST.

George RA, Heringa J.

Proteins. 2002 Sep 1;48(4):672-81.

PMID:
12211035
14.

Combined prediction of transmembrane topology and signal peptide of beta-barrel proteins: using a hidden Markov model and genetic algorithms.

Zou L, Wang Z, Wang Y, Hu F.

Comput Biol Med. 2010 Jul;40(7):621-8. doi: 10.1016/j.compbiomed.2010.04.006. Epub 2010 May 21.

PMID:
20488436
15.

Protein family classification and functional annotation.

Wu CH, Huang H, Yeh LS, Barker WC.

Comput Biol Chem. 2003 Feb;27(1):37-47. Review.

PMID:
12798038
16.

Sequence-based protein structure prediction using a reduced state-space hidden Markov model.

Lampros C, Costas Papaloukas, Exarchos TP, Yorgos Goletsis, Fotiadis DI.

Comput Biol Med. 2007 Sep;37(9):1211-24. Epub 2006 Dec 11.

PMID:
17161834
17.

Protein comparison at the domain architecture level.

Lee B, Lee D.

BMC Bioinformatics. 2009 Dec 3;10 Suppl 15:S5. doi: 10.1186/1471-2105-10-S15-S5.

18.

Internal gene duplication in the evolution of prokaryotic transmembrane proteins.

Shimizu T, Mitsuke H, Noto K, Arai M.

J Mol Biol. 2004 May 21;339(1):1-15.

PMID:
15123416
20.

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