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Results: 1 to 20 of 899

1.

A structure-based method for protein sequence alignment.

Kann MG, Thiessen PA, Panchenko AR, Schäffer AA, Altschul SF, Bryant SH.

Bioinformatics. 2005 Apr 15;21(8):1451-6. Epub 2004 Dec 21.

PMID:
15613392
[PubMed - indexed for MEDLINE]
Free Article
2.

COBALT: constraint-based alignment tool for multiple protein sequences.

Papadopoulos JS, Agarwala R.

Bioinformatics. 2007 May 1;23(9):1073-9. Epub 2007 Mar 1.

PMID:
17332019
[PubMed - indexed for MEDLINE]
Free Article
3.

CORAL: aligning conserved core regions across domain families.

Fong JH, Marchler-Bauer A.

Bioinformatics. 2009 Aug 1;25(15):1862-8. doi: 10.1093/bioinformatics/btp334. Epub 2009 May 26.

PMID:
19470584
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.

PMID:
17883866
[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.

Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues.

Anand B, Gowri VS, Srinivasan N.

Bioinformatics. 2005 Jun 15;21(12):2821-6. Epub 2005 Apr 7.

PMID:
15817691
[PubMed - indexed for MEDLINE]
Free Article
7.

MulPSSM: a database of multiple position-specific scoring matrices of protein domain families.

Gowri VS, Krishnadev O, Swamy CS, Srinivasan N.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D243-6.

PMID:
16381855
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Prediction of functional specificity determinants from protein sequences using log-likelihood ratios.

Pei J, Cai W, Kinch LN, Grishin NV.

Bioinformatics. 2006 Jan 15;22(2):164-71. Epub 2005 Nov 8.

PMID:
16278237
[PubMed - indexed for MEDLINE]
Free Article
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
[PubMed - indexed for MEDLINE]
Free Article
11.

Comparison of sequence and structure alignments for protein domains.

Marchler-Bauer A, Panchenko AR, Ariel N, Bryant SH.

Proteins. 2002 Aug 15;48(3):439-46.

PMID:
12112669
[PubMed - indexed for MEDLINE]
12.

A new progressive-iterative algorithm for multiple structure alignment.

Lupyan D, Leo-Macias A, Ortiz AR.

Bioinformatics. 2005 Aug 1;21(15):3255-63. Epub 2005 Jun 7.

PMID:
15941743
[PubMed - indexed for MEDLINE]
Free Article
13.

DbW: automatic update of a functional family-specific multiple alignment.

Prigent V, Thierry JC, Poch O, Plewniak F.

Bioinformatics. 2005 Apr 15;21(8):1437-42. Epub 2004 Dec 14.

PMID:
15598832
[PubMed - indexed for MEDLINE]
Free Article
14.

Automatic prediction of protein domains from sequence information using a hybrid learning system.

Nagarajan N, Yona G.

Bioinformatics. 2004 Jun 12;20(9):1335-60. Epub 2004 Feb 12.

PMID:
14962932
[PubMed - indexed for MEDLINE]
Free Article
15.

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
16.

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
[PubMed - indexed for MEDLINE]
17.

AL2CO: calculation of positional conservation in a protein sequence alignment.

Pei J, Grishin NV.

Bioinformatics. 2001 Aug;17(8):700-12.

PMID:
11524371
[PubMed - indexed for MEDLINE]
Free Article
18.

Tools for integrated sequence-structure analysis with UCSF Chimera.

Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE.

BMC Bioinformatics. 2006 Jul 12;7:339.

PMID:
16836757
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

SAD--a normalized structural alignment database: improving sequence-structure alignments.

Marsden B, Abagyan R.

Bioinformatics. 2004 Oct 12;20(15):2333-44. Epub 2004 Apr 15.

PMID:
15087320
[PubMed - indexed for MEDLINE]
Free Article
20.

Refining multiple sequence alignments with conserved core regions.

Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH.

Nucleic Acids Res. 2006 May 17;34(9):2598-606. Print 2006.

PMID:
16707662
[PubMed - indexed for MEDLINE]
Free PMC Article

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