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Items: 1 to 20 of 91

1.

Protein domain assignment from the recurrence of locally similar structures.

Tai CH, Sam V, Gibrat JF, Garnier J, Munson PJ, Lee B.

Proteins. 2011 Mar;79(3):853-66. doi: 10.1002/prot.22923. Epub 2010 Dec 22.

2.

dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment.

Alden K, Veretnik S, Bourne PE.

BMC Bioinformatics. 2010 Jun 9;11:310. doi: 10.1186/1471-2105-11-310.

3.

Protein structural domains: analysis of the 3Dee domains database.

Dengler U, Siddiqui AS, Barton GJ.

Proteins. 2001 Feb 15;42(3):332-44.

PMID:
11151005
4.

Toward consistent assignment of structural domains in proteins.

Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN.

J Mol Biol. 2004 Jun 4;339(3):647-78.

PMID:
15147847
5.

Intrinsic disorder in the Protein Data Bank.

Le Gall T, Romero PR, Cortese MS, Uversky VN, Dunker AK.

J Biomol Struct Dyn. 2007 Feb;24(4):325-42.

PMID:
17206849
6.

CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

Redfern OC, Harrison A, Dallman T, Pearl FM, Orengo CA.

PLoS Comput Biol. 2007 Nov;3(11):e232.

7.

A 3D sequence-independent representation of the protein data bank.

Fischer D, Tsai CJ, Nussinov R, Wolfson H.

Protein Eng. 1995 Oct;8(10):981-97.

PMID:
8771179
8.

Domain assignment for protein structures using a consensus approach: characterization and analysis.

Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM.

Protein Sci. 1998 Feb;7(2):233-42.

9.

Recognizing the fold of a protein structure.

Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C.

Bioinformatics. 2003 Sep 22;19(14):1748-59.

PMID:
14512345
10.
11.

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.

Martin J, Letellier G, Marin A, Taly JF, de Brevern AG, Gibrat JF.

BMC Struct Biol. 2005 Sep 15;5:17.

12.

Analysis of domain structural class using an automated class assignment protocol.

Michie AD, Orengo CA, Thornton JM.

J Mol Biol. 1996 Sep 20;262(2):168-85.

PMID:
8831787
13.

Identification and analysis of domains in proteins.

Islam SA, Luo J, Sternberg MJ.

Protein Eng. 1995 Jun;8(6):513-25.

PMID:
8532675
14.

A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.

Day R, Beck DA, Armen RS, Daggett V.

Protein Sci. 2003 Oct;12(10):2150-60.

15.

Towards an intelligent system for the automatic assignment of domains in globular proteins.

Sternberg MJ, Hegyi H, Islam SA, Luo J, Russell RB.

Proc Int Conf Intell Syst Mol Biol. 1995;3:376-83.

PMID:
7584461
16.

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
17.

Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner.

Gutiérrez FI, Rodriguez-Valenzuela F, Ibarra IL, Devos DP, Melo F.

BMC Bioinformatics. 2016 Jan 5;17:20. doi: 10.1186/s12859-015-0866-8.

18.

Structure-based functional inference in structural genomics.

Kim SH, Shin DH, Choi IG, Schulze-Gahmen U, Chen S, Kim R.

J Struct Funct Genomics. 2003;4(2-3):129-35. Review.

PMID:
14649297
19.

Supra-domains: evolutionary units larger than single protein domains.

Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA.

J Mol Biol. 2004 Feb 20;336(3):809-23.

PMID:
15095989
20.

Structural characteristics of novel protein folds.

Fernandez-Fuentes N, Dybas JM, Fiser A.

PLoS Comput Biol. 2010 Apr 22;6(4):e1000750. doi: 10.1371/journal.pcbi.1000750.

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