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Results: 1 to 20 of 127

1.

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison.

Ortiz AR, Strauss CE, Olmea O.

Protein Sci. 2002 Nov;11(11):2606-21.

PMID:
12381844
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G.

BMC Bioinformatics. 2007 Jul 13;8:252.

PMID:
17629909
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A new progressive-iterative algorithm for multiple structure alignment.

Lupyan D, Leo-Macias A, Ortiz AR.

Bioinformatics. 2005 Aug 1;21(15):3255-63. Epub 2005 Jun 7.

PMID:
15941743
[PubMed - indexed for MEDLINE]
Free Article
4.

Detailed protein sequence alignment based on Spectral Similarity Score (SSS).

Gupta K, Thomas D, Vidya SV, Venkatesh KV, Ramakumar S.

BMC Bioinformatics. 2005 Apr 23;6:105.

PMID:
15850477
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Improving the accuracy of protein secondary structure prediction using structural alignment.

Montgomerie S, Sundararaj S, Gallin WJ, Wishart DS.

BMC Bioinformatics. 2006 Jun 14;7:301.

PMID:
16774686
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs.

Randall A, Baldi P.

BMC Struct Biol. 2008 Dec 3;8:52. doi: 10.1186/1472-6807-8-52.

PMID:
19055744
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.

Pandit SB, Skolnick J.

BMC Bioinformatics. 2008 Dec 12;9:531. doi: 10.1186/1471-2105-9-531.

PMID:
19077267
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
[PubMed - indexed for MEDLINE]
Free Article
9.

DescFold: a web server for protein fold recognition.

Yan RX, Si JN, Wang C, Zhang Z.

BMC Bioinformatics. 2009 Dec 14;10:416. doi: 10.1186/1471-2105-10-416.

PMID:
20003426
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Predicting functional sites with an automated algorithm suitable for heterogeneous datasets.

La D, Livesay DR.

BMC Bioinformatics. 2005 May 13;6:116.

PMID:
15890082
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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]
13.

MODBASE, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22.

PMID:
14681398
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Improving the quality of twilight-zone alignments.

Jaroszewski L, Rychlewski L, Godzik A.

Protein Sci. 2000 Aug;9(8):1487-96.

PMID:
10975570
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ.

BMC Bioinformatics. 2003 Oct 10;4:47.

PMID:
14552658
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Tools for integrated sequence-structure analysis with UCSF Chimera.

Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE.

BMC Bioinformatics. 2006 Jul 12;7:339.

PMID:
16836757
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Protein structure prediction based on sequence similarity.

Jaroszewski L.

Methods Mol Biol. 2009;569:129-56. doi: 10.1007/978-1-59745-524-4_7.

PMID:
19623489
[PubMed - indexed for MEDLINE]
18.

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
[PubMed - indexed for MEDLINE]
19.

FAST: a novel protein structure alignment algorithm.

Zhu J, Weng Z.

Proteins. 2005 Feb 15;58(3):618-27.

PMID:
15609341
[PubMed - indexed for MEDLINE]
20.

Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment.

Venclovas C, Margelevicius M.

Proteins. 2005;61 Suppl 7:99-105.

PMID:
16187350
[PubMed - indexed for MEDLINE]

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