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Protein sequence and structure alignments within one framework.

Schenk G, Margraf T, Torda AE.

Algorithms Mol Biol. 2008 Apr 1;3:4.PMID: 18380904 [PubMed]Related articlesFree article

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.PMID: 19077267 [PubMed - indexed for MEDLINE]Related articlesFree article

Sequence-similar, structure-dissimilar protein pairs in the PDB.

Kosloff M, Kolodny R.

Proteins. 2008 May 1;71(2):891-902.PMID: 18004789 [PubMed - indexed for MEDLINE]Related articlesFree article

The structural alignment between two proteins: is there a unique answer?

Godzik A.

Protein Sci. 1996 Jul;5(7):1325-38.PMID: 8819165 [PubMed - indexed for MEDLINE]Related articlesFree article

Evaluation of sequence alignments of distantly related sequence pairs with respect to structural similarity.

Gürler A, Knapp EW.

Genome Inform. 2007;18:183-91.PMID: 18546486 [PubMed - indexed for MEDLINE]Related articlesFree article

Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions.

Hvidsten TR, Kryshtafovych A, Fidelis K.

Proteins. 2009 Jun;75(4):870-84.PMID: 19025980 [PubMed - indexed for MEDLINE]Related articles

Analysis on sliding helices and strands in protein structural comparisons: a case study with protein kinases.

Gowri VS, Anamika K, Gore S, Srinivasan N.

J Biosci. 2007 Aug;32(5):921-8.PMID: 17914234 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistical significance in biological sequence analysis.

Mitrophanov AY, Borodovsky M.

Brief Bioinform. 2006 Mar;7(1):2-24. Review.PMID: 16761361 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving protein structure similarity searches using domain boundaries based on conserved sequence information.

Thompson KE, Wang Y, Madej T, Bryant SH.

BMC Struct Biol. 2009 May 19;9:33.PMID: 19454035 [PubMed - indexed for MEDLINE]Related articlesFree article

SE: an algorithm for deriving sequence alignment from a pair of superimposed structures.

Tai CH, Vincent JJ, Kim C, Lee B.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S4.PMID: 19208141 [PubMed - indexed for MEDLINE]Related articlesFree article

A comprehensive analysis of non-sequential alignments between all protein structures.

Abyzov A, Ilyin VA.

BMC Struct Biol. 2007 Nov 16;7:78.PMID: 18005453 [PubMed - indexed for MEDLINE]Related articlesFree article

Structural alphabets for protein structure classification: a comparison study.

Le Q, Pollastri G, Koehl P.

J Mol Biol. 2009 Mar 27;387(2):431-50. Epub 2008 Dec 25.PMID: 19135454 [PubMed - indexed for MEDLINE]Related articles

Iterative refinement of structure-based sequence alignments by Seed Extension.

Kim C, Tai CH, Lee B.

BMC Bioinformatics. 2009 Jul 9;10:210.PMID: 19589133 [PubMed - indexed for MEDLINE]Related articlesFree article

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.

Katoh K, Toh H.

BMC Bioinformatics. 2008 Apr 25;9:212.PMID: 18439255 [PubMed - indexed for MEDLINE]Related articlesFree article

Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties.

Tong W, Wei Y, Murga LF, Ondrechen MJ, Williams RJ.

PLoS Comput Biol. 2009 Jan;5(1):e1000266. Epub 2009 Jan 16.PMID: 19148270 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein structure alignment considering phenotypic plasticity.

Csaba G, Birzele F, Zimmer R.

Bioinformatics. 2008 Aug 15;24(16):i98-104.PMID: 18689847 [PubMed - indexed for MEDLINE]Related articlesFree article

Flexible secondary structure based protein structure comparison applied to the detection of circular permutation.

Vesterstrøm J, Taylor WR.

J Comput Biol. 2006 Jan-Feb;13(1):43-63.PMID: 16472021 [PubMed - indexed for MEDLINE]Related articles

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. Epub 2009 Mar 13.PMID: 19293946 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrated search and alignment of protein structures.

Sacan A, Toroslu IH, Ferhatosmanoglu H.

Bioinformatics. 2008 Dec 15;24(24):2872-9. Epub 2008 Oct 22.PMID: 18945684 [PubMed - indexed for MEDLINE]Related articlesFree article

The SALAMI protein structure search server.

Margraf T, Schenk G, Torda AE.

Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W480-4. Epub 2009 May 22.PMID: 19465380 [PubMed - indexed for MEDLINE]Related articlesFree article