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Links from PubMed

Items: 1 to 20 of 149

1.

Pfam: a comprehensive database of protein domain families based on seed alignments.

Sonnhammer EL, Eddy SR, Durbin R.

Proteins. 1997 Jul;28(3):405-20.

PMID:
9223186
2.

Pfam: multiple sequence alignments and HMM-profiles of protein domains.

Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R.

Nucleic Acids Res. 1998 Jan 1;26(1):320-2.

3.

Exhaustive enumeration of protein domain families.

Heger A, Holm L.

J Mol Biol. 2003 May 2;328(3):749-67.

PMID:
12706730
4.

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL.

Nucleic Acids Res. 1999 Jan 1;27(1):260-2.

5.

Identifying protein domains with the Pfam database.

Coggill P, Finn RD, Bateman A.

Curr Protoc Bioinformatics. 2008 Sep;Chapter 2:Unit 2.5. doi: 10.1002/0471250953.bi0205s23.

PMID:
18819075
6.

PIR-ALN: a database of protein sequence alignments.

Srinivasarao GY, Yeh LS, Marzec CR, Orcutt BC, Barker WC.

Bioinformatics. 1999 May;15(5):382-90.

7.

The PAS fold. A redefinition of the PAS domain based upon structural prediction.

Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J.

Eur J Biochem. 2004 Mar;271(6):1198-208.

PMID:
15009198
8.

A kingdom-specific protein domain HMM library for improved annotation of fungal genomes.

Alam I, Hubbard SJ, Oliver SG, Rattray M.

BMC Genomics. 2007 Apr 10;8:97.

9.

Identifying protein domains with the Pfam database.

Finn R, Griffiths-Jones S, Bateman A.

Curr Protoc Bioinformatics. 2003 May;Chapter 2:Unit 2.5. doi: 10.1002/0471250953.bi0205s01.

PMID:
18428696
10.

webPRC: the Profile Comparer for alignment-based searching of public domain databases.

Brandt BW, Heringa J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W48-52. doi: 10.1093/nar/gkp279. Epub 2009 May 6.

11.

Analysis of protein domain families in Caenorhabditis elegans.

Sonnhammer EL, Durbin R.

Genomics. 1997 Dec 1;46(2):200-16.

PMID:
9417907
14.

A sequence alignment-independent method for protein classification.

Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I.

Appl Bioinformatics. 2004;3(2-3):137-48.

PMID:
15693739
15.
16.

ProClass Protein Family Database.

Wu CH, Shivakumar S, Huang H.

Nucleic Acids Res. 1999 Jan 1;27(1):272-4.

17.

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
18.

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.

Dietmann S, Park J, Notredame C, Heger A, Lappe M, Holm L.

Nucleic Acids Res. 2001 Jan 1;29(1):55-7.

19.

The TIGRFAMs database of protein families.

Haft DH, Selengut JD, White O.

Nucleic Acids Res. 2003 Jan 1;31(1):371-3.

20.

Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.

Henikoff S, Henikoff JG, Pietrokovski S.

Bioinformatics. 1999 Jun;15(6):471-9.

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