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Items: 20

1.

A series of PDB related databases for everyday needs.

Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R, Sander C, Vriend G.

Nucleic Acids Res. 2011 Jan;39(Database issue):D411-9. doi: 10.1093/nar/gkq1105. Epub 2010 Nov 11.

2.

deconSTRUCT: general purpose protein database search on the substructure level.

Zhang ZH, Bharatham K, Sherman WA, Mihalek I.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W590-4. doi: 10.1093/nar/gkq489. Epub 2010 Jun 3.

3.

Novel protein folds and their nonsequential structural analogs.

Guerler A, Knapp EW.

Protein Sci. 2008 Aug;17(8):1374-82. doi: 10.1110/ps.035469.108. Epub 2008 Jun 26.

4.

Efficient parameterized algorithms for biopolymer structure-sequence alignment.

Song Y, Liu C, Huang X, Malmberg RL, Xu Y, Cai L.

IEEE/ACM Trans Comput Biol Bioinform. 2006 Oct-Dec;3(4):423-32.

PMID:
17085850
5.

FAST: a novel protein structure alignment algorithm.

Zhu J, Weng Z.

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

PMID:
15609341
6.

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.

Krissinel E, Henrick K.

Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68. Epub 2004 Nov 26.

PMID:
15572779
7.

SABmark--a benchmark for sequence alignment that covers the entire known fold space.

Van Walle I, Lasters I, Wyns L.

Bioinformatics. 2005 Apr 1;21(7):1267-8. Epub 2004 Aug 27.

PMID:
15333456
8.

TOPS: an enhanced database of protein structural topology.

Michalopoulos I, Torrance GM, Gilbert DR, Westhead DR.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D251-4.

9.

Multiple structural alignment by secondary structures: algorithm and applications.

Dror O, Benyamini H, Nussinov R, Wolfson HJ.

Protein Sci. 2003 Nov;12(11):2492-507.

10.

MASS: multiple structural alignment by secondary structures.

Dror O, Benyamini H, Nussinov R, Wolfson H.

Bioinformatics. 2003;19 Suppl 1:i95-104.

PMID:
12855444
12.

Detection of non-topological motifs in protein structures.

Alesker V, Nussinov R, Wolfson HJ.

Protein Eng. 1996 Dec;9(12):1103-19.

PMID:
9010924
13.
14.

An algorithm for finding maximal common subtopologies in a set of protein structures.

Koch I, Lengauer T, Wanke E.

J Comput Biol. 1996 Summer;3(2):289-306.

PMID:
8811488
15.

Surprising similarities in structure comparison.

Gibrat JF, Madej T, Bryant SH.

Curr Opin Struct Biol. 1996 Jun;6(3):377-85. Review.

PMID:
8804824
16.

Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

Grindley HM, Artymiuk PJ, Rice DW, Willett P.

J Mol Biol. 1993 Feb 5;229(3):707-21.

PMID:
8381875
17.

Protein structure comparison by alignment of distance matrices.

Holm L, Sander C.

J Mol Biol. 1993 Sep 5;233(1):123-38.

PMID:
8377180
18.

3-D lookup: fast protein structure database searches at 90% reliability.

Holm L, Sander C.

Proc Int Conf Intell Syst Mol Biol. 1995;3:179-87.

PMID:
7584435
19.

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Kabsch W, Sander C.

Biopolymers. 1983 Dec;22(12):2577-637. No abstract available.

PMID:
6667333
20.

Use of techniques derived from graph theory to compare secondary structure motifs in proteins.

Mitchell EM, Artymiuk PJ, Rice DW, Willett P.

J Mol Biol. 1990 Mar 5;212(1):151-66.

PMID:
2319595

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