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Items: 1 to 20 of 482

1.

The meaning of alignment: lessons from structural diversity.

Pirovano W, Feenstra KA, Heringa J.

BMC Bioinformatics. 2008 Dec 23;9:556. doi: 10.1186/1471-2105-9-556.

3.

MUSTANG: a multiple structural alignment algorithm.

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

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

PMID:
16736488
4.

FAST: a novel protein structure alignment algorithm.

Zhu J, Weng Z.

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

PMID:
15609341
5.

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
6.

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
7.

QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure.

Suhrer SJ, Gruber M, Sippl MJ.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W411-5. Epub 2007 May 3.

8.

Multiple flexible structure alignment using partial order graphs.

Ye Y, Godzik A.

Bioinformatics. 2005 May 15;21(10):2362-9. Epub 2005 Mar 3.

PMID:
15746292
9.

Analysis and prediction of functional sub-types from protein sequence alignments.

Hannenhalli SS, Russell RB.

J Mol Biol. 2000 Oct 13;303(1):61-76.

PMID:
11021970
10.

FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.

Saini HK, Fischer D.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W499-502. Epub 2007 May 30.

11.

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.

Pirovano W, Feenstra KA, Heringa J.

Bioinformatics. 2008 Feb 15;24(4):492-7. doi: 10.1093/bioinformatics/btm636. Epub 2008 Jan 2.

PMID:
18174178
12.

From analysis of protein structural alignments toward a novel approach to align protein sequences.

Sunyaev SR, Bogopolsky GA, Oleynikova NV, Vlasov PK, Finkelstein AV, Roytberg MA.

Proteins. 2004 Feb 15;54(3):569-82.

PMID:
14748004
13.

A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues.

Capriotti E, Fariselli P, Rossi I, Casadio R.

Proteins. 2004 Feb 1;54(2):351-60.

PMID:
14696197
14.

Fast model-based protein homology detection without alignment.

Hochreiter S, Heusel M, Obermayer K.

Bioinformatics. 2007 Jul 15;23(14):1728-36. Epub 2007 May 8.

PMID:
17488755
15.

A generalized affine gap model significantly improves protein sequence alignment accuracy.

Zachariah MA, Crooks GE, Holbrook SR, Brenner SE.

Proteins. 2005 Feb 1;58(2):329-38.

PMID:
15562515
16.

Towards a reliable objective function for multiple sequence alignments.

Thompson JD, Plewniak F, Ripp R, Thierry JC, Poch O.

J Mol Biol. 2001 Dec 7;314(4):937-51.

PMID:
11734009
17.

Multiple sequence alignments.

Wallace IM, Blackshields G, Higgins DG.

Curr Opin Struct Biol. 2005 Jun;15(3):261-6. Review.

PMID:
15963889
18.

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.

19.

Align: a C++ class library and web server for rapid sequence alignment prototyping.

Tosatto SC, Albiero A, Mantovan A, Ferrari C, Bindewald E, Toppo S.

Curr Drug Discov Technol. 2006 Sep;3(3):167-73.

PMID:
17311562
20.

Iterative non-sequential protein structural alignment.

Salem S, Zaki MJ, Bystroff C.

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

PMID:
19507290

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