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Results: 1 to 20 of 138

1.

MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments.

Minami S, Sawada K, Chikenji G.

BMC Bioinformatics. 2013 Jan 18;14:24. doi: 10.1186/1471-2105-14-24.

PMID:
23331634
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Connectivity independent protein-structure alignment: a hierarchical approach.

Kolbeck B, May P, Schmidt-Goenner T, Steinke T, Knapp EW.

BMC Bioinformatics. 2006 Nov 21;7:510.

PMID:
17118190
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Multiple structure alignment with msTALI.

Shealy P, Valafar H.

BMC Bioinformatics. 2012 May 20;13:105. doi: 10.1186/1471-2105-13-105.

PMID:
22607234
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Biological insights from topology independent comparison of protein 3D structures.

Nguyen MN, Madhusudhan MS.

Nucleic Acids Res. 2011 Aug;39(14):e94. doi: 10.1093/nar/gkr348. Epub 2011 May 19.

PMID:
21596786
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Comparative analysis of protein structure alignments.

Mayr G, Domingues FS, Lackner P.

BMC Struct Biol. 2007 Jul 26;7:50.

PMID:
17672887
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins.

Yuan X, Bystroff C.

Bioinformatics. 2005 Apr 1;21(7):1010-9. Epub 2004 Nov 5.

PMID:
15531601
[PubMed - indexed for MEDLINE]
Free Article
7.

Iterative non-sequential protein structural alignment.

Salem S, Zaki MJ, Bystroff C.

J Bioinform Comput Biol. 2009 Jun;7(3):571-96.

PMID:
19507290
[PubMed - indexed for MEDLINE]
8.

FlexSnap: flexible non-sequential protein structure alignment.

Salem S, Zaki MJ, Bystroff C.

Algorithms Mol Biol. 2010 Jan 4;5:12. doi: 10.1186/1748-7188-5-12.

PMID:
20047669
[PubMed]
Free PMC Article
9.

Matt: local flexibility aids protein multiple structure alignment.

Menke M, Berger B, Cowen L.

PLoS Comput Biol. 2008 Jan;4(1):e10. doi: 10.1371/journal.pcbi.0040010.

PMID:
18193941
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

MUSTANG: a multiple structural alignment algorithm.

Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM.

Proteins. 2006 Aug 15;64(3):559-74.

PMID:
16736488
[PubMed - indexed for MEDLINE]
11.

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
[PubMed - indexed for MEDLINE]
12.

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH.

Teichert F, Minning J, Bastolla U, Porto M.

BMC Bioinformatics. 2010 May 14;11:251. doi: 10.1186/1471-2105-11-251.

PMID:
20470364
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

SANA: an algorithm for sequential and non-sequential protein structure alignment.

Wang L, Wu LY, Wang Y, Zhang XS, Chen L.

Amino Acids. 2010 Jul;39(2):417-25. doi: 10.1007/s00726-009-0457-y. Epub 2010 Feb 2.

PMID:
20127263
[PubMed - indexed for MEDLINE]
14.

SISYPHUS--structural alignments for proteins with non-trivial relationships.

Andreeva A, Prlić A, Hubbard TJ, Murzin AG.

Nucleic Acids Res. 2007 Jan;35(Database issue):D253-9. Epub 2006 Oct 26.

PMID:
17068077
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
14573862
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.

Chen L, Wu LY, Wang Y, Zhang S, Zhang XS.

BMC Struct Biol. 2006 Sep 2;6:18.

PMID:
16948858
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

MASS: multiple structural alignment by secondary structures.

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

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

PMID:
12855444
[PubMed - indexed for MEDLINE]
Free Article
18.

Large-scale comparison of protein sequence alignment algorithms with structure alignments.

Sauder JM, Arthur JW, Dunbrack RL Jr.

Proteins. 2000 Jul 1;40(1):6-22.

PMID:
10813826
[PubMed - indexed for MEDLINE]
19.

A novel method to compare protein structures using local descriptors.

Daniluk P, Lesyng B.

BMC Bioinformatics. 2011 Aug 17;12:344. doi: 10.1186/1471-2105-12-344.

PMID:
21849047
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures.

Shih ES, Gan RC, Hwang MJ.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W95-8.

PMID:
16845117
[PubMed - indexed for MEDLINE]
Free PMC Article

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