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Items: 1 to 20 of 155

1.

Structural alphabets for protein structure classification: a comparison study.

Le Q, Pollastri G, Koehl P.

J Mol Biol. 2009 Mar 27;387(2):431-50. doi: 10.1016/j.jmb.2008.12.044. Epub 2008 Dec 25.

2.

Discovery of structural motifs using protein structural alphabets and 1D motif-finding methods.

Ku SY, Hu YJ.

Adv Exp Med Biol. 2010;680:117-23. doi: 10.1007/978-1-4419-5913-3_14.

PMID:
20865493
3.

Automated alphabet reduction for protein datasets.

Bacardit J, Stout M, Hirst JD, Valencia A, Smith RE, Krasnogor N.

BMC Bioinformatics. 2009 Jan 6;10:6. doi: 10.1186/1471-2105-10-6.

4.

Mining protein loops using a structural alphabet and statistical exceptionality.

Regad L, Martin J, Nuel G, Camproux AC.

BMC Bioinformatics. 2010 Feb 4;11:75. doi: 10.1186/1471-2105-11-75.

5.

Prediction of protein structural classes for low-homology sequences based on predicted secondary structure.

Yang JY, Peng ZL, Chen X.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S9. doi: 10.1186/1471-2105-11-S1-S9.

6.

Methods for optimizing the structure alphabet sequences of proteins.

Dong QW, Wang XL, Lin L.

Comput Biol Med. 2007 Nov;37(11):1610-6. Epub 2007 May 10.

PMID:
17493604
7.
8.

Protein structure mining using a structural alphabet.

Tyagi M, de Brevern AG, Srinivasan N, Offmann B.

Proteins. 2008 May 1;71(2):920-37.

PMID:
18004784
9.

Recognizing the fold of a protein structure.

Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C.

Bioinformatics. 2003 Sep 22;19(14):1748-59.

PMID:
14512345
10.

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.

11.

Designing succinct structural alphabets.

Li SC, Bu D, Gao X, Xu J, Li M.

Bioinformatics. 2008 Jul 1;24(13):i182-9. doi: 10.1093/bioinformatics/btn165.

12.

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.

13.

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

Pascual-García A, Abia D, Ortiz AR, Bastolla U.

PLoS Comput Biol. 2009 Mar;5(3):e1000331. doi: 10.1371/journal.pcbi.1000331. Epub 2009 Mar 27.

14.

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
15.

SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

Kurgan L, Cios K, Chen K.

BMC Bioinformatics. 2008 May 1;9:226. doi: 10.1186/1471-2105-9-226.

17.

Protein structure search and local structure characterization.

Ku SY, Hu YJ.

BMC Bioinformatics. 2008 Aug 22;9:349. doi: 10.1186/1471-2105-9-349.

18.
19.

Use of a structural alphabet to find compatible folds for amino acid sequences.

Mahajan S, de Brevern AG, Sanejouand YH, Srinivasan N, Offmann B.

Protein Sci. 2015 Jan;24(1):145-53. doi: 10.1002/pro.2581. Epub 2014 Oct 25.

20.

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