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Items: 1 to 20 of 126

1.

LGA: A method for finding 3D similarities in protein structures.

Zemla A.

Nucleic Acids Res. 2003 Jul 1;31(13):3370-4.

2.

AS2TS system for protein structure modeling and analysis.

Zemla A, Zhou CE, Slezak T, Kuczmarski T, Rama D, Torres C, Sawicka D, Barsky D.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W111-5.

3.

Search similar protein structures with classification, sequence and 3d alignments.

Lu Z, Zhao Z, Garcia S, Krishnaswamy K, Fu B.

J Bioinform Comput Biol. 2009 Oct;7(5):755-71.

PMID:
19785044
4.

MATRAS: A program for protein 3D structure comparison.

Kawabata T.

Nucleic Acids Res. 2003 Jul 1;31(13):3367-9.

5.

STRALCP--structure alignment-based clustering of proteins.

Zemla A, Geisbrecht B, Smith J, Lam M, Kirkpatrick B, Wagner M, Slezak T, Zhou CE.

Nucleic Acids Res. 2007;35(22):e150. Epub 2007 Nov 26.

6.

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.

7.

Integrated search and alignment of protein structures.

Sacan A, Toroslu IH, Ferhatosmanoglu H.

Bioinformatics. 2008 Dec 15;24(24):2872-9. doi: 10.1093/bioinformatics/btn545. Epub 2008 Oct 22.

PMID:
18945684
8.

CAALIGN: a program for pairwise and multiple protein-structure alignment.

Oldfield TJ.

Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):514-25. Epub 2007 Mar 16.

PMID:
17372357
9.

FAST: a novel protein structure alignment algorithm.

Zhu J, Weng Z.

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

PMID:
15609341
10.

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
11.

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.

Arnold K, Bordoli L, Kopp J, Schwede T.

Bioinformatics. 2006 Jan 15;22(2):195-201. Epub 2005 Nov 13.

PMID:
16301204
12.

Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.

Lehtonen JV, Denessiouk K, May AC, Johnson MS.

Proteins. 1999 Feb 15;34(3):341-55.

PMID:
10024021
13.

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
14.

The ProDom database of protein domain families: more emphasis on 3D.

Bru C, Courcelle E, Carrère S, Beausse Y, Dalmar S, Kahn D.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D212-5.

15.

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
16.

Clustering the annotation space of proteins.

Kunin V, Ouzounis CA.

BMC Bioinformatics. 2005 Feb 9;6:24.

17.

HCPM--program for hierarchical clustering of protein models.

Gront D, Kolinski A.

Bioinformatics. 2005 Jul 15;21(14):3179-80. Epub 2005 Apr 19.

PMID:
15840705
18.

Measuring the similarity of protein structures by means of the universal similarity metric.

Krasnogor N, Pelta DA.

Bioinformatics. 2004 May 1;20(7):1015-21. Epub 2004 Jan 29.

PMID:
14751983
19.

SAD--a normalized structural alignment database: improving sequence-structure alignments.

Marsden B, Abagyan R.

Bioinformatics. 2004 Oct 12;20(15):2333-44. Epub 2004 Apr 15.

PMID:
15087320
20.

Motif3D: Relating protein sequence motifs to 3D structure.

Gaulton A, Attwood TK.

Nucleic Acids Res. 2003 Jul 1;31(13):3333-6.

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