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Results: 1 to 20 of 134

1.

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction.

Yan R, Xu D, Yang J, Walker S, Zhang Y.

Sci Rep. 2013;3:2619. doi: 10.1038/srep02619.

PMID:
24018415
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

DescFold: a web server for protein fold recognition.

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

BMC Bioinformatics. 2009 Dec 14;10:416. doi: 10.1186/1471-2105-10-416.

PMID:
20003426
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
19077267
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Improving the quality of twilight-zone alignments.

Jaroszewski L, Rychlewski L, Godzik A.

Protein Sci. 2000 Aug;9(8):1487-96.

PMID:
10975570
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Alignment of protein sequences by their profiles.

Marti-Renom MA, Madhusudhan MS, Sali A.

Protein Sci. 2004 Apr;13(4):1071-87.

PMID:
15044736
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

(PS)2-v2: template-based protein structure prediction server.

Chen CC, Hwang JK, Yang JM.

BMC Bioinformatics. 2009 Oct 31;10:366. doi: 10.1186/1471-2105-10-366.

PMID:
19878598
[PubMed - indexed for MEDLINE]
Free PMC Article
7.
8.

Sequence comparison and protein structure prediction.

Dunbrack RL Jr.

Curr Opin Struct Biol. 2006 Jun;16(3):374-84. Epub 2006 May 19. Review.

PMID:
16713709
[PubMed - indexed for MEDLINE]
9.

Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.

Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K.

Proteins. 2003 Jun 1;51(4):504-14.

PMID:
12784210
[PubMed - indexed for MEDLINE]
10.

Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment.

Venclovas C, Margelevicius M.

Proteins. 2005;61 Suppl 7:99-105.

PMID:
16187350
[PubMed - indexed for MEDLINE]
11.

Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction.

Scheeff ED, Bourne PE.

BMC Bioinformatics. 2006 Sep 14;7:410.

PMID:
16970830
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
20470364
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
[PubMed - indexed for MEDLINE]
Free Article
14.

TM-align: a protein structure alignment algorithm based on the TM-score.

Zhang Y, Skolnick J.

Nucleic Acids Res. 2005 Apr 22;33(7):2302-9. Print 2005.

PMID:
15849316
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Local structure-based sequence profile database for local and global protein structure predictions.

Yang AS, Wang LY.

Bioinformatics. 2002 Dec;18(12):1650-7.

PMID:
12490450
[PubMed - indexed for MEDLINE]
Free Article
16.

Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection.

Jung I, Lee J, Lee SY, Kim D.

BMC Bioinformatics. 2008 Jul 1;9:298. doi: 10.1186/1471-2105-9-298.

PMID:
18590572
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
[PubMed - indexed for MEDLINE]
18.

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.

PMID:
22163274
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Profile-profile alignment: a powerful tool for protein structure prediction.

von Ohsen N, Sommer I, Zimmer R.

Pac Symp Biocomput. 2003:252-63.

PMID:
12603033
[PubMed - indexed for MEDLINE]
20.

PSSM-based prediction of DNA binding sites in proteins.

Ahmad S, Sarai A.

BMC Bioinformatics. 2005 Feb 19;6:33.

PMID:
15720719
[PubMed - indexed for MEDLINE]
Free PMC Article

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