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Results: 1 to 20 of 1000

1.

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
[PubMed - indexed for MEDLINE]
2.

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.

Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM.

Bioinformatics. 2000 Nov;16(11):988-1002.

PMID:
11159310
[PubMed - indexed for MEDLINE]
Free Article
3.

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments.

Gough J, Chothia C.

Nucleic Acids Res. 2002 Jan 1;30(1):268-72.

PMID:
11752312
[PubMed - indexed for MEDLINE]
Free PMC Article
4.
5.

Exhaustive enumeration of protein domain families.

Heger A, Holm L.

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

PMID:
12706730
[PubMed - indexed for MEDLINE]
6.

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.

PMID:
20686689
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Conservation and specialization in PAS domain dynamics.

Pandini A, Bonati L.

Protein Eng Des Sel. 2005 Mar;18(3):127-37. Epub 2005 Apr 8.

PMID:
15820977
[PubMed - indexed for MEDLINE]
Free Article
8.

PAS domains. Common structure and common flexibility.

Vreede J, van der Horst MA, Hellingwerf KJ, Crielaard W, van Aalten DM.

J Biol Chem. 2003 May 16;278(20):18434-9. Epub 2003 Mar 14.

PMID:
12639952
[PubMed - indexed for MEDLINE]
Free Article
9.

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
[PubMed - indexed for MEDLINE]
10.

Amino acid recognition by Venus flytrap domains is encoded in an 8-residue motif.

Acher FC, Bertrand HO.

Biopolymers. 2005;80(2-3):357-66.

PMID:
15810013
[PubMed - indexed for MEDLINE]
11.

DPANN: improved sequence to structure alignments following fold recognition.

Reinhardt A, Eisenberg D.

Proteins. 2004 Aug 15;56(3):528-38.

PMID:
15229885
[PubMed - indexed for MEDLINE]
12.

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.

PMID:
9399864
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes.

Pandit SB, Gosar D, Abhiman S, Sujatha S, Dixit SS, Mhatre NS, Sowdhamini R, Srinivasan N.

Nucleic Acids Res. 2002 Jan 1;30(1):289-93.

PMID:
11752317
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

Protein structure mining using a structural alphabet.

Tyagi M, de Brevern AG, Srinivasan N, Offmann B.

Proteins. 2008 May 1;71(2):920-37.

PMID:
18004784
[PubMed - indexed for MEDLINE]
17.

Database of homology-derived protein structures and the structural meaning of sequence alignment.

Sander C, Schneider R.

Proteins. 1991;9(1):56-68.

PMID:
2017436
[PubMed - indexed for MEDLINE]
18.

Structural genomics of Caenorhabditis elegans: crystal structure of the tropomodulin C-terminal domain.

Lu S, Symersky J, Li S, Carson M, Chen L, Meehan E, Luo M.

Proteins. 2004 Aug 1;56(2):384-6. No abstract available.

PMID:
15211521
[PubMed - indexed for MEDLINE]
19.

Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.

Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K.

BMC Struct Biol. 2007 Jun 20;7:40.

PMID:
17584917
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The HSSP database of protein structure-sequence alignments.

Sander C, Schneider R.

Nucleic Acids Res. 1994 Sep;22(17):3597-9.

PMID:
7937066
[PubMed - indexed for MEDLINE]
Free PMC Article

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