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Items: 1 to 20 of 35

1.

CDD: specific functional annotation with the Conserved Domain Database.

Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH.

Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10. doi: 10.1093/nar/gkn845. Epub 2008 Nov 4.

2.

Automated protein subfamily identification and classification.

Brown DP, Krishnamurthy N, Sjölander K.

PLoS Comput Biol. 2007 Aug;3(8):e160.

3.

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment.

Kann MG, Sheetlin SL, Park Y, Bryant SH, Spouge JL.

Nucleic Acids Res. 2007;35(14):4678-85. Epub 2007 Jun 27.

4.

The SUPERFAMILY database in 2007: families and functions.

Wilson D, Madera M, Vogel C, Chothia C, Gough J.

Nucleic Acids Res. 2007 Jan;35(Database issue):D308-13. Epub 2006 Nov 10.

5.

Refining multiple sequence alignments with conserved core regions.

Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH.

Nucleic Acids Res. 2006 May 17;34(9):2598-606. Print 2006.

6.

SMART 5: domains in the context of genomes and networks.

Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D257-60.

7.

Pfam: clans, web tools and services.

Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51.

9.

A structure-based method for protein sequence alignment.

Kann MG, Thiessen PA, Panchenko AR, Schäffer AA, Altschul SF, Bryant SH.

Bioinformatics. 2005 Apr 15;21(8):1451-6. Epub 2004 Dec 21.

PMID:
15613392
10.

Protein homology detection by HMM-HMM comparison.

Söding J.

Bioinformatics. 2005 Apr 1;21(7):951-60. Epub 2004 Nov 5. Erratum in: Bioinformatics. 2005 May 1;21(9):2144.

PMID:
15531603
11.

SABmark--a benchmark for sequence alignment that covers the entire known fold space.

Van Walle I, Lasters I, Wyns L.

Bioinformatics. 2005 Apr 1;21(7):1267-8. Epub 2004 Aug 27.

PMID:
15333456
12.
13.

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Edgar RC.

Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. Print 2004.

14.

A comparison of scoring functions for protein sequence profile alignment.

Edgar RC, Sjölander K.

Bioinformatics. 2004 May 22;20(8):1301-8. Epub 2004 Feb 12.

PMID:
14962936
15.

Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments.

Mittelman D, Sadreyev R, Grishin N.

Bioinformatics. 2003 Aug 12;19(12):1531-9.

PMID:
12912834
16.

Profile-profile alignment: a powerful tool for protein structure prediction.

von Ohsen N, Sommer I, Zimmer R.

Pac Symp Biocomput. 2003:252-63.

17.
18.

Finding weak similarities between proteins by sequence profile comparison.

Panchenko AR.

Nucleic Acids Res. 2003 Jan 15;31(2):683-9.

19.
20.

CDD: a database of conserved domain alignments with links to domain three-dimensional structure.

Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH.

Nucleic Acids Res. 2002 Jan 1;30(1):281-3.

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