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Tableau-based protein substructure search using quadratic programming.

Stivala A, Wirth A, Stuckey PJ.

BMC Bioinformatics. 2009 May 19;10:153.PMID: 19450287 [PubMed - indexed for MEDLINE]Related articlesFree article

Structural search and retrieval using a tableau representation of protein folding patterns.

Konagurthu AS, Stuckey PJ, Lesk AM.

Bioinformatics. 2008 Mar 1;24(5):645-51. Epub 2008 Jan 5.PMID: 18175768 [PubMed - indexed for MEDLINE]Related articlesFree article

Alignment of protein interaction networks by integer quadratic programming.

Li Z, Wang Y, Zhang S, Zhang XS, Chen L.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5527-30.PMID: 17945906 [PubMed - indexed for MEDLINE]Related articles

Contact patterns between helices and strands of sheet define protein folding patterns.

Kamat AP, Lesk AM.

Proteins. 2007 Mar 1;66(4):869-76.PMID: 17206659 [PubMed - indexed for MEDLINE]Related articles

Solving structures of protein complexes by molecular replacement with Phaser.

McCoy AJ.

Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.PMID: 17164524 [PubMed - indexed for MEDLINE]Related articlesFree article

Constraint Logic Programming approach to protein structure prediction.

Dal Palù A, Dovier A, Fogolari F.

BMC Bioinformatics. 2004 Nov 30;5:186.PMID: 15571634 [PubMed - indexed for MEDLINE]Related articlesFree article

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

Karpenahalli MR, Lupas AN, Söding J.

BMC Bioinformatics. 2007 Jan 3;8:2.PMID: 17199898 [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

FLORA: a novel method to predict protein function from structure in diverse superfamilies.

Redfern OC, Dessailly BH, Dallman TJ, Sillitoe I, Orengo CA.

PLoS Comput Biol. 2009 Aug;5(8):e1000485. Epub 2009 Aug 28.PMID: 19714201 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns.

Tseng YY, Dundas J, Liang J.

J Mol Biol. 2009 Mar 27;387(2):451-64. Epub 2009 Jan 6.PMID: 19154742 [PubMed - indexed for MEDLINE]Related articles

Guiding conformation space search with an all-atom energy potential.

Brunette TJ, Brock O.

Proteins. 2008 Dec;73(4):958-72.PMID: 18536015 [PubMed - indexed for MEDLINE]Related articlesFree article

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database.

Ginzinger SW, Coles M.

J Biomol NMR. 2009 Mar;43(3):179-85. Epub 2009 Feb 18.PMID: 19224375 [PubMed - indexed for MEDLINE]Related articles

Bayesian nonparametric model for the validation of peptide identification in shotgun proteomics.

Zhang J, Ma J, Dou L, Wu S, Qian X, Xie H, Zhu Y, He F.

Mol Cell Proteomics. 2009 Mar;8(3):547-57. Epub 2008 Nov 12.PMID: 19005226 [PubMed - indexed for MEDLINE]Related articles

ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.

Shi S, Chitturi B, Grishin NV.

Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W526-31. Epub 2009 May 6.PMID: 19420061 [PubMed - indexed for MEDLINE]Related articlesFree article

Mining super-secondary structure motifs from 3d protein structures: a sequence order independent approach.

Aung Z, Li J.

Genome Inform. 2007;19:15-26.PMID: 18546501 [PubMed - indexed for MEDLINE]Related articlesFree article

Remote homology detection using a kernel method that combines sequence and secondary-structure similarity scores.

Wieser D, Niranjan M.

In Silico Biol. 2009;9(3):89-103.PMID: 19795568 [PubMed - indexed for MEDLINE]Related articles

PLIPS, an automatically collected database of protein lists reported by proteomics studies.

Antonov AV, Dietmann S, Wong P, Igor R, Mewes HW.

J Proteome Res. 2009 Mar;8(3):1193-7.PMID: 19216535 [PubMed - indexed for MEDLINE]Related articles

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

Prediction of beta-turn in protein using E-SSpred and support vector machine.

Liu L, Fang Y, Li M, Wang C.

Protein J. 2009 May;28(3-4):175-81.PMID: 19488840 [PubMed - indexed for MEDLINE]Related articles

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines.

Jones AR, Siepen JA, Hubbard SJ, Paton NW.

Proteomics. 2009 Mar;9(5):1220-9.PMID: 19253293 [PubMed - indexed for MEDLINE]Related articles