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Results: 1 to 20 of 208

1.

Context-specific amino acid substitution matrices and their use in the detection of protein homologs.

Goonesekere NC, Lee B.

Proteins. 2008 May 1;71(2):910-9.

PMID:
18004781
[PubMed - indexed for MEDLINE]
2.

An amino acid substitution matrix for protein conformation identification.

Liu X, Zheng WM.

J Bioinform Comput Biol. 2006 Jun;4(3):769-82.

PMID:
16960974
[PubMed - indexed for MEDLINE]
3.

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
4.

A transition probability model for amino acid substitutions from blocks.

Veerassamy S, Smith A, Tillier ER.

J Comput Biol. 2003;10(6):997-1010.

PMID:
14980022
[PubMed - indexed for MEDLINE]
5.

A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins.

Brick K, Pizzi E.

BMC Bioinformatics. 2008 May 16;9:236. doi: 10.1186/1471-2105-9-236.

PMID:
18485187
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments.

Gelly JC, Chiche L, Gracy J.

BMC Bioinformatics. 2005 Jan 10;6:4.

PMID:
15638949
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Protein database searches using compositionally adjusted substitution matrices.

Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schäffer AA, Yu YK.

FEBS J. 2005 Oct;272(20):5101-9. Review.

PMID:
16218944
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

Yona G, Levitt M.

J Mol Biol. 2002 Feb 1;315(5):1257-75.

PMID:
11827492
[PubMed - indexed for MEDLINE]
9.

Protein domain identification and improved sequence similarity searching using PSI-BLAST.

George RA, Heringa J.

Proteins. 2002 Sep 1;48(4):672-81.

PMID:
12211035
[PubMed - indexed for MEDLINE]
10.
11.

Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

Tan YH, Huang H, Kihara D.

Proteins. 2006 Aug 15;64(3):587-600.

PMID:
16799934
[PubMed - indexed for MEDLINE]
12.

Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins.

Baussand J, Deremble C, Carbone A.

Proteins. 2007 May 15;67(3):695-708.

PMID:
17299747
[PubMed - indexed for MEDLINE]
13.

Aligning protein sequence and analysing substitution pattern using a class-specific matrix.

Xu HS, Ren WK, Liu XH, Li XQ.

J Biosci. 2010 Jun;35(2):295-314.

PMID:
20689185
[PubMed - indexed for MEDLINE]
Free Article
14.

Performance evaluation of amino acid substitution matrices.

Henikoff S, Henikoff JG.

Proteins. 1993 Sep;17(1):49-61.

PMID:
8234244
[PubMed - indexed for MEDLINE]
15.

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
[PubMed - indexed for MEDLINE]
16.

ProFAT: a web-based tool for the functional annotation of protein sequences.

Bradshaw CR, Surendranath V, Habermann B.

BMC Bioinformatics. 2006 Oct 23;7:466.

PMID:
17059594
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Use of residue pairs in protein sequence-sequence and sequence-structure alignments.

Jung J, Lee B.

Protein Sci. 2000 Aug;9(8):1576-88.

PMID:
10975579
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance.

Agrawal A, Huang X.

Bioinformatics. 2009 Apr 15;25(8):1082-3. doi: 10.1093/bioinformatics/btp089. Epub 2009 Feb 27.

PMID:
19251771
[PubMed - indexed for MEDLINE]
Free Article
19.

Sequence context-specific profiles for homology searching.

Biegert A, Söding J.

Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3770-5. doi: 10.1073/pnas.0810767106. Epub 2009 Feb 20.

PMID:
19234132
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Ulla: a program for calculating environment-specific amino acid substitution tables.

Lee S, Blundell TL.

Bioinformatics. 2009 Aug 1;25(15):1976-7. doi: 10.1093/bioinformatics/btp300. Epub 2009 May 5.

PMID:
19417059
[PubMed - indexed for MEDLINE]
Free PMC Article

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