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Items: 1 to 20 of 611

1.

Incremental window-based protein sequence alignment algorithms.

Rangwala H, Karypis G.

Bioinformatics. 2007 Jan 15;23(2):e17-23.

PMID:
17237087
2.

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
3.

A comparison of scoring functions for protein sequence profile alignment.

Edgar RC, Sjölander K.

Bioinformatics. 2004 May 22;20(8):1301-8. Epub 2004 Feb 12.

PMID:
14962936
4.

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
5.

Profile-based string kernels for remote homology detection and motif extraction.

Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C.

J Bioinform Comput Biol. 2005 Jun;3(3):527-50.

PMID:
16108083
6.

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.

7.

COACH: profile-profile alignment of protein families using hidden Markov models.

Edgar RC, Sjölander K.

Bioinformatics. 2004 May 22;20(8):1309-18. Epub 2004 Feb 12.

PMID:
14962937
8.
9.

Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms.

Poleksic A, Fienup M.

Bioinformatics. 2008 May 1;24(9):1145-53. doi: 10.1093/bioinformatics/btn097. Epub 2008 Mar 12.

PMID:
18337259
10.

PROMALS: towards accurate multiple sequence alignments of distantly related proteins.

Pei J, Grishin NV.

Bioinformatics. 2007 Apr 1;23(7):802-8. Epub 2007 Jan 31.

PMID:
17267437
11.

Predicting reliable regions in protein alignments from sequence profiles.

Tress ML, Jones D, Valencia A.

J Mol Biol. 2003 Jul 18;330(4):705-18.

PMID:
12850141
12.

SVM-HUSTLE--an iterative semi-supervised machine learning approach for pairwise protein remote homology detection.

Shah AR, Oehmen CS, Webb-Robertson BJ.

Bioinformatics. 2008 Mar 15;24(6):783-90. doi: 10.1093/bioinformatics/btn028. Epub 2008 Feb 1.

PMID:
18245127
13.

Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.

Kundrotas PJ, Lensink MF, Alexov E.

Int J Biol Macromol. 2008 Aug 15;43(2):198-208. doi: 10.1016/j.ijbiomac.2008.05.004. Epub 2008 May 21.

PMID:
18572239
14.

Protein homology detection using string alignment kernels.

Saigo H, Vert JP, Ueda N, Akutsu T.

Bioinformatics. 2004 Jul 22;20(11):1682-9. Epub 2004 Feb 26.

PMID:
14988126
15.

Comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments.

Wang C, Yan RX, Wang XF, Si JN, Zhang Z.

Comput Biol Chem. 2011 Oct 12;35(5):308-18. doi: 10.1016/j.compbiolchem.2011.07.006. Epub 2011 Jul 22.

PMID:
22000802
16.

Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT).

Lee MM, Bundschuh R, Chan MK.

Proteins. 2008 May 15;71(3):1409-19.

PMID:
18076050
17.
18.

Homology-extended sequence alignment.

Simossis VA, Kleinjung J, Heringa J.

Nucleic Acids Res. 2005 Feb 7;33(3):816-24. Print 2005.

19.

ESyPred3D: Prediction of proteins 3D structures.

Lambert C, Léonard N, De Bolle X, Depiereux E.

Bioinformatics. 2002 Sep;18(9):1250-6.

PMID:
12217917
20.

A Novel algorithm for identifying low-complexity regions in a protein sequence.

Li X, Kahveci T.

Bioinformatics. 2006 Dec 15;22(24):2980-7. Epub 2006 Oct 2.

PMID:
17018537

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