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Items: 1 to 20 of 798

1.

Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.

Lin HN, Notredame C, Chang JM, Sung TY, Hsu WL.

PLoS One. 2011;6(12):e27872. doi: 10.1371/journal.pone.0027872. Epub 2011 Dec 2.

2.

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.

3.

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.

4.

Adaptive Smith-Waterman residue match seeding for protein structural alignment.

Topham CM, Rouquier M, Tarrat N, André I.

Proteins. 2013 Oct;81(10):1823-39. doi: 10.1002/prot.24327. Epub 2013 Aug 19.

PMID:
23720362
5.

Structure-dependent sequence alignment for remotely related proteins.

Yang AS.

Bioinformatics. 2002 Dec;18(12):1658-65.

PMID:
12490451
6.

AL2CO: calculation of positional conservation in a protein sequence alignment.

Pei J, Grishin NV.

Bioinformatics. 2001 Aug;17(8):700-12.

PMID:
11524371
8.

Stochastic pairwise alignments.

Mückstein U, Hofacker IL, Stadler PF.

Bioinformatics. 2002;18 Suppl 2:S153-60.

PMID:
12385998
9.

DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.

Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B.

BMC Bioinformatics. 2005 Mar 22;6:66.

10.

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.

11.

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
12.
13.

Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions.

Huang YM, Bystroff C.

Bioinformatics. 2006 Feb 15;22(4):413-22. Epub 2005 Dec 13.

PMID:
16352653
14.

Improving protein secondary structure prediction based on short subsequences with local structure similarity.

Lin HN, Sung TY, Ho SY, Hsu WL.

BMC Genomics. 2010 Dec 2;11 Suppl 4:S4. doi: 10.1186/1471-2164-11-S4-S4.

15.

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.

16.

Vorolign--fast structural alignment using Voronoi contacts.

Birzele F, Gewehr JE, Csaba G, Zimmer R.

Bioinformatics. 2007 Jan 15;23(2):e205-11.

PMID:
17237093
17.

Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.

Domingues FS, Lackner P, Andreeva A, Sippl MJ.

J Mol Biol. 2000 Apr 7;297(4):1003-13.

PMID:
10736233
18.

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.

Liu Y, Schmidt B, Maskell DL.

Bioinformatics. 2010 Aug 15;26(16):1958-64. doi: 10.1093/bioinformatics/btq338. Epub 2010 Jun 23.

PMID:
20576627
19.

Rapid similarity search of proteins using alignments of domain arrangements.

Terrapon N, Weiner J, Grath S, Moore AD, Bornberg-Bauer E.

Bioinformatics. 2014 Jan 15;30(2):274-81. doi: 10.1093/bioinformatics/btt379. Epub 2013 Jul 4.

PMID:
23828785
20.

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

Terashi G, Takeda-Shitaka M.

PLoS One. 2015 Oct 26;10(10):e0141440. doi: 10.1371/journal.pone.0141440. eCollection 2015.

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