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Items: 1 to 20 of 189

1.

Transmembrane proteins in the Protein Data Bank: identification and classification.

Tusnády GE, Dosztányi Z, Simon I.

Bioinformatics. 2004 Nov 22;20(17):2964-72. Epub 2004 Jun 4.

2.

TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates.

Tusnády GE, Dosztányi Z, Simon I.

Bioinformatics. 2005 Apr 1;21(7):1276-7. Epub 2004 Nov 11.

3.

PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank.

Tusnády GE, Dosztányi Z, Simon I.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D275-8.

4.

PDBTM: Protein Data Bank of transmembrane proteins after 8 years.

Kozma D, Simon I, Tusnády GE.

Nucleic Acids Res. 2013 Jan;41(Database issue):D524-9. doi: 10.1093/nar/gks1169. Epub 2012 Nov 30.

5.

OPM: orientations of proteins in membranes database.

Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI.

Bioinformatics. 2006 Mar 1;22(5):623-5. Epub 2006 Jan 5.

6.

Enhanced recognition of protein transmembrane domains with prediction-based structural profiles.

Cao B, Porollo A, Adamczak R, Jarrell M, Meller J.

Bioinformatics. 2006 Feb 1;22(3):303-9. Epub 2005 Nov 17.

7.

Computational differentiation of N-terminal signal peptides and transmembrane helices.

Yuan Z, Davis MJ, Zhang F, Teasdale RD.

Biochem Biophys Res Commun. 2003 Dec 26;312(4):1278-83.

PMID:
14652012
8.

Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins.

Bagos PG, Liakopoulos TD, Hamodrakas SJ.

BMC Bioinformatics. 2006 Apr 5;7:189.

9.

PIBASE: a comprehensive database of structurally defined protein interfaces.

Davis FP, Sali A.

Bioinformatics. 2005 May 1;21(9):1901-7. Epub 2005 Jan 18.

10.

Transmembrane helix prediction using amino acid property features and latent semantic analysis.

Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J.

BMC Bioinformatics. 2008;9 Suppl 1:S4. doi: 10.1186/1471-2105-9-S1-S4.

11.
12.

TOPDOM: database of domains and motifs with conservative location in transmembrane proteins.

Tusnády GE, Kalmár L, Hegyi H, Tompa P, Simon I.

Bioinformatics. 2008 Jun 15;24(12):1469-70. doi: 10.1093/bioinformatics/btn202. Epub 2008 Apr 23.

13.

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins.

Martelli PL, Fariselli P, Krogh A, Casadio R.

Bioinformatics. 2002;18 Suppl 1:S46-53.

14.

A periodicity analysis of transmembrane helices.

Leonov H, Arkin IT.

Bioinformatics. 2005 Jun 1;21(11):2604-10. Epub 2005 Mar 3.

15.

A simple statistical method for discriminating outer membrane proteins with better accuracy.

Gromiha MM, Suwa M.

Bioinformatics. 2005 Apr 1;21(7):961-8. Epub 2004 Nov 5.

16.

Classification of transmembrane segments in human proteins using wavelet-based energy.

Kitsas IK, Hadjileontiadis LJ, Panas SM.

Conf Proc IEEE Eng Med Biol Soc. 2007;2007:1225-8.

PMID:
18002184
17.

STAM: simple transmembrane alignment method.

Shafrir Y, Guy HR.

Bioinformatics. 2004 Mar 22;20(5):758-69. Epub 2004 Jan 29.

18.

TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.

Cserzo M, Eisenhaber F, Eisenhaber B, Simon I.

Bioinformatics. 2004 Jan 1;20(1):136-7.

19.

ProtBuD: a database of biological unit structures of protein families and superfamilies.

Xu Q, Canutescu A, Obradovic Z, Dunbrack RL Jr.

Bioinformatics. 2006 Dec 1;22(23):2876-82. Epub 2006 Oct 2. Erratum in: Bioinformatics. 2007 Aug;23(15):2028.

20.

A computational pipeline for protein structure prediction and analysis at genome scale.

Shah M, Passovets S, Kim D, Ellrott K, Wang L, Vokler I, LoCascio P, Xu D, Xu Y.

Bioinformatics. 2003 Oct 12;19(15):1985-96.

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