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Items: 1 to 20 of 114

1.

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

Kolodny R, Koehl P, Levitt M.

J Mol Biol. 2005 Mar 4;346(4):1173-88. Epub 2005 Jan 16.

2.

Sensitivity and selectivity in protein structure comparison.

Sierk ML, Pearson WR.

Protein Sci. 2004 Mar;13(3):773-85.

3.

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.

4.

Structure alignment based on coding of local geometric measures.

Chang PL, Rinne AW, Dewey TG.

BMC Bioinformatics. 2006 Jul 14;7:346.

5.

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G.

BMC Bioinformatics. 2007 Jul 13;8:252.

6.

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.

7.

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.

8.

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.

9.

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.

10.

Comparative analysis of protein structure alignments.

Mayr G, Domingues FS, Lackner P.

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

11.

An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites.

Pang B, Schlessman D, Kuang X, Zhao N, Shyu D, Korkin D, Shyu CR.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Mar-Apr;12(2):298-308. doi: 10.1109/TCBB.2014.2355208.

PMID:
26357218
12.

Pareto optimal pairwise sequence alignment.

DeRonne KW, Karypis G.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):481-93. doi: 10.1109/TCBB.2013.2.

PMID:
23929871
13.

DALIX: optimal DALI protein structure alignment.

Wohlers I, Andonov R, Klau GW.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):26-36. doi: 10.1109/TCBB.2012.143.

PMID:
23702541
14.

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.

Daniels NM, Nadimpalli S, Cowen LJ.

BMC Bioinformatics. 2012 Oct 6;13:259. doi: 10.1186/1471-2105-13-259.

15.

ASH structure alignment package: sensitivity and selectivity in domain classification.

Standley DM, Toh H, Nakamura H.

BMC Bioinformatics. 2007 Apr 4;8:116.

16.

Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments.

Sierk ML, Smoot ME, Bass EJ, Pearson WR.

BMC Bioinformatics. 2010 Mar 22;11:146. doi: 10.1186/1471-2105-11-146.

17.

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.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

Tong J, Pei J, Grishin NV.

BMC Bioinformatics. 2015 Sep 3;16:282. doi: 10.1186/s12859-015-0711-0.

20.

A comprehensive system for evaluation of remote sequence similarity detection.

Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV.

BMC Bioinformatics. 2007 Aug 28;8:314.

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