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Items: 1 to 20 of 55

1.

A practical guide for the computational selection of residues to be experimentally characterized in protein families.

Benítez-Páez A, Cárdenas-Brito S, Gutiérrez AJ.

Brief Bioinform. 2012 May;13(3):329-36. doi: 10.1093/bib/bbr052. Epub 2011 Sep 19. Review.

PMID:
21930656
2.
3.

Using information theory to search for co-evolving residues in proteins.

Martin LC, Gloor GB, Dunn SD, Wahl LM.

Bioinformatics. 2005 Nov 15;21(22):4116-24. Epub 2005 Sep 13.

PMID:
16159918
4.

State-of-the-art bioinformatics protein structure prediction tools (Review).

Pavlopoulou A, Michalopoulos I.

Int J Mol Med. 2011 Sep;28(3):295-310. doi: 10.3892/ijmm.2011.705. Epub 2011 May 23. Review.

PMID:
21617841
5.
6.

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N.

Proteins. 2005 Feb 15;58(3):610-7.

PMID:
15614759
7.

Phylogeny-independent detection of functional residues.

Pazos F, Rausell A, Valencia A.

Bioinformatics. 2006 Jun 15;22(12):1440-8. Epub 2006 Mar 21.

PMID:
16551661
8.

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification.

Sankararaman S, Sjölander K.

Bioinformatics. 2008 Nov 1;24(21):2445-52. doi: 10.1093/bioinformatics/btn474. Epub 2008 Sep 6.

10.

WSsas: a web service for the annotation of functional residues through structural homologues.

Talavera D, Laskowski RA, Thornton JM.

Bioinformatics. 2009 May 1;25(9):1192-4. doi: 10.1093/bioinformatics/btp116. Epub 2009 Feb 27.

PMID:
19251774
11.

Blast sampling for structural and functional analyses.

Friedrich A, Ripp R, Garnier N, Bettler E, Deléage G, Poch O, Moulinier L.

BMC Bioinformatics. 2007 Feb 23;8:62.

12.

Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins.

Mihalek I, Res I, Lichtarge O.

Proteins. 2006 Apr 1;63(1):87-99.

PMID:
16397893
13.

Model-based prediction of sequence alignment quality.

Ahola V, Aittokallio T, Vihinen M, Uusipaikka E.

Bioinformatics. 2008 Oct 1;24(19):2165-71. doi: 10.1093/bioinformatics/btn414. Epub 2008 Aug 4.

PMID:
18678587
14.

Practical analysis of specificity-determining residues in protein families.

Chagoyen M, García-Martín JA, Pazos F.

Brief Bioinform. 2016 Mar;17(2):255-61. doi: 10.1093/bib/bbv045. Epub 2015 Jul 2. Review.

PMID:
26141829
15.

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.

Landgraf R, Xenarios I, Eisenberg D.

J Mol Biol. 2001 Apr 13;307(5):1487-502.

PMID:
11292355
16.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
17.

Computational methods for protein sequence comparison and search.

Xu D.

Curr Protoc Protein Sci. 2009 Apr;Chapter 2:Unit2.1. doi: 10.1002/0471140864.ps0201s56.

PMID:
19365790
18.
19.

Entropy calculator: getting the best from your multiple protein alignments.

Ramazzotti M, Degl'Innocenti D, Manao G, Ramponi G.

Ital J Biochem. 2004 Mar;53(1):16-22.

PMID:
15356957
20.

Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules.

Fober T, Mernberger M, Klebe G, Hüllermeier E.

Bioinformatics. 2009 Aug 15;25(16):2110-7. doi: 10.1093/bioinformatics/btp144. Epub 2009 Mar 13.

PMID:
19286830

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