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Results: 1 to 20 of 115

1.

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.

Apeltsin L, Morris JH, Babbitt PC, Ferrin TE.

Bioinformatics. 2011 Feb 1;27(3):326-33. doi: 10.1093/bioinformatics/btq655. Epub 2010 Nov 29.

PMID:
21118823
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.

Wittkop T, Baumbach J, Lobo FP, Rahmann S.

BMC Bioinformatics. 2007 Oct 17;8:396.

PMID:
17941985
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19325884
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space.

Loewenstein Y, Portugaly E, Fromer M, Linial M.

Bioinformatics. 2008 Jul 1;24(13):i41-9. doi: 10.1093/bioinformatics/btn174.

PMID:
18586742
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

PMID:
12386002
[PubMed - indexed for MEDLINE]
Free Article
6.

Towards automatic clustering of protein sequences.

Yang J, Wang W.

Proc IEEE Comput Soc Bioinform Conf. 2002;1:175-86.

PMID:
15838134
[PubMed - indexed for MEDLINE]
7.

Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles.

Bhattacharya A, De RK.

Bioinformatics. 2008 Jun 1;24(11):1359-66. doi: 10.1093/bioinformatics/btn133. Epub 2008 Apr 10.

PMID:
18407922
[PubMed - indexed for MEDLINE]
Free Article
8.

Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property.

Zhong W, Altun G, Harrison R, Tai PC, Pan Y.

IEEE Trans Nanobioscience. 2005 Sep;4(3):255-65.

PMID:
16220690
[PubMed - indexed for MEDLINE]
9.

SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.

Nepusz T, Sasidharan R, Paccanaro A.

BMC Bioinformatics. 2010 Mar 9;11:120. doi: 10.1186/1471-2105-11-120.

PMID:
20214776
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.

PMID:
17570145
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A new similarity measure among protein sequences.

Wu KP, Lin HN, Sung TY, Hsu WL.

Proc IEEE Comput Soc Bioinform Conf. 2003;2:347-52.

PMID:
16452810
[PubMed - indexed for MEDLINE]
12.

A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets.

Sharma A, Podolsky R, Zhao J, McIndoe RA.

Bioinformatics. 2009 May 1;25(9):1152-7. doi: 10.1093/bioinformatics/btp123. Epub 2009 Mar 4.

PMID:
19261720
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
18452616
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A network clustering algorithm for detection of protein families.

Xie J, Wang M, Dai D, Zhang H, Zhang W.

Conf Proc IEEE Eng Med Biol Soc. 2012;2012:6329-32. doi: 10.1109/EMBC.2012.6347441.

PMID:
23367376
[PubMed - indexed for MEDLINE]
15.

Bayesian search of functionally divergent protein subgroups and their function specific residues.

Marttinen P, Corander J, Törönen P, Holm L.

Bioinformatics. 2006 Oct 15;22(20):2466-74. Epub 2006 Jul 26.

PMID:
16870932
[PubMed - indexed for MEDLINE]
Free Article
16.

A novel approach for clustering proteomics data using Bayesian fast Fourier transform.

Bensmail H, Golek J, Moody MM, Semmes JO, Haoudi A.

Bioinformatics. 2005 May 15;21(10):2210-24. Epub 2005 Mar 15.

PMID:
15769836
[PubMed - indexed for MEDLINE]
Free Article
17.

Clustering-based approach for predicting motif pairs from protein interaction data.

Leung HC, Siu MH, Yiu SM, Chin FY, Sung KW.

J Bioinform Comput Biol. 2009 Aug;7(4):701-16.

PMID:
19634199
[PubMed - indexed for MEDLINE]
18.

Functionally guided alignment of protein interaction networks for module detection.

Ali W, Deane CM.

Bioinformatics. 2009 Dec 1;25(23):3166-73. doi: 10.1093/bioinformatics/btp569. Epub 2009 Oct 1.

PMID:
19797409
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

CLUSS: clustering of protein sequences based on a new similarity measure.

Kelil A, Wang S, Brzezinski R, Fleury A.

BMC Bioinformatics. 2007 Aug 4;8:286.

PMID:
17683581
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Searching remote homology with spectral clustering with symmetry in neighborhood cluster kernels.

Maulik U, Sarkar A.

PLoS One. 2013;8(2):e46468. doi: 10.1371/journal.pone.0046468. Epub 2013 Feb 15.

PMID:
23457439
[PubMed - indexed for MEDLINE]
Free PMC Article

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