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Items: 1 to 50 of 125

1.

Statistical inference of protein structural alignments using information and compression.

Collier JH, Allison L, Lesk AM, Stuckey PJ, Garcia de la Banda M, Konagurthu AS.

Bioinformatics. 2017 Apr 1;33(7):1005-1013. doi: 10.1093/bioinformatics/btw757.

PMID:
28065899
2.

On sufficient statistics of least-squares superposition of vector sets.

Konagurthu AS, Kasarapu P, Allison L, Collier JH, Lesk AM.

J Comput Biol. 2015 Jun;22(6):487-97. doi: 10.1089/cmb.2014.0154. Epub 2015 Feb 19.

PMID:
25695500
3.

A new statistical framework to assess structural alignment quality using information compression.

Collier JH, Allison L, Lesk AM, Garcia de la Banda M, Konagurthu AS.

Bioinformatics. 2014 Sep 1;30(17):i512-8. doi: 10.1093/bioinformatics/btu460.

4.

How precise are reported protein coordinate data?

Konagurthu AS, Allison L, Abramson D, Stuckey PJ, Lesk AM.

Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):904-6. doi: 10.1107/S1399004713031787. Epub 2014 Feb 27.

PMID:
24598758
5.

Sizes of interface residues account for cross-class binding affinity patterns in Eph receptor-ephrin families.

Guo FY, Lesk AM.

Proteins. 2014 Mar;82(3):349-53. doi: 10.1002/prot.24414. Epub 2013 Oct 18.

PMID:
24105818
6.

Comment on "Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments" by C. Micheletti.

Lesk AM.

Phys Life Rev. 2013 Mar;10(1):33-4; discussion 39-40. doi: 10.1016/j.plrev.2012.10.007. Epub 2012 Oct 26. No abstract available.

PMID:
23154220
7.

Structure description and identification using the tableau representation of protein folding patterns.

Konagurthu AS, Lesk AM.

Methods Mol Biol. 2013;932:51-9. doi: 10.1007/978-1-62703-065-6_4.

PMID:
22987346
8.

Minimum message length inference of secondary structure from protein coordinate data.

Konagurthu AS, Lesk AM, Allison L.

Bioinformatics. 2012 Jun 15;28(12):i97-105. doi: 10.1093/bioinformatics/bts223.

9.

Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank.

Collier JH, Lesk AM, Garcia de la Banda M, Konagurthu AS.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W334-9. doi: 10.1093/nar/gks436. Epub 2012 May 25.

10.

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).

Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, Hardie RA, Woodbridge P, Tindall EA, Bertelsen MF, Dixon D, Pyecroft S, Helgen KM, Lesk AM, Pringle TH, Patterson N, Zhang Y, Kreiss A, Woods GM, Jones ME, Schuster SC.

Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12348-53. doi: 10.1073/pnas.1102838108. Epub 2011 Jun 27. Erratum in: Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18625.

11.

Piecewise linear approximation of protein structures using the principle of minimum message length.

Konagurthu AS, Allison L, Stuckey PJ, Lesk AM.

Bioinformatics. 2011 Jul 1;27(13):i43-51. doi: 10.1093/bioinformatics/btr240.

12.

MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography.

Konagurthu AS, Reboul CF, Schmidberger JW, Irving JA, Lesk AM, Stuckey PJ, Whisstock JC, Buckle AM.

PLoS One. 2010 Apr 6;5(4):e10048. doi: 10.1371/journal.pone.0010048.

13.

Cataloging topologies of protein folding patterns.

Konagurthu AS, Lesk AM.

J Mol Recognit. 2010 Mar-Apr;23(2):253-7. doi: 10.1002/jmr.1006. Review.

PMID:
20151416
14.

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).

Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MT, Dalén L, Arsuaga JL, Ericson PG, Huson DH, Helgen KM, Murphy WJ, Götherström A, Schuster SC.

Genome Res. 2009 Feb;19(2):213-20. doi: 10.1101/gr.082628.108. Epub 2009 Jan 12.

15.

Sequencing the nuclear genome of the extinct woolly mammoth.

Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, Knight JR, Irzyk GP, Fredrikson KM, Harkins TT, Sheridan S, Pringle T, Schuster SC.

Nature. 2008 Nov 20;456(7220):387-90. doi: 10.1038/nature07446.

PMID:
19020620
16.

On the origin of distribution patterns of motifs in biological networks.

Konagurthu AS, Lesk AM.

BMC Syst Biol. 2008 Aug 12;2:73. doi: 10.1186/1752-0509-2-73.

17.

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes.

Gilbert MT, Drautz DI, Lesk AM, Ho SY, Qi J, Ratan A, Hsu CH, Sher A, Dalén L, Götherström A, Tomsho LP, Rendulic S, Packard M, Campos PF, Kuznetsova TV, Shidlovskiy F, Tikhonov A, Willerslev E, Iacumin P, Buigues B, Ericson PG, Germonpré M, Kosintsev P, Nikolaev V, Nowak-Kemp M, Knight JR, Irzyk GP, Perbost CS, Fredrikson KM, Harkins TT, Sheridan S, Miller W, Schuster SC.

Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8327-32. doi: 10.1073/pnas.0802315105. Epub 2008 Jun 9.

18.

Single and multiple input modules in regulatory networks.

Konagurthu AS, Lesk AM.

Proteins. 2008 Nov 1;73(2):320-4. doi: 10.1002/prot.22053.

PMID:
18433061
19.

Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families.

Zen A, Carnevale V, Lesk AM, Micheletti C.

Protein Sci. 2008 May;17(5):918-29. doi: 10.1110/ps.073390208. Epub 2008 Mar 27.

20.

On the use of overlapping lattices for screening to find pairs of nearby points in two and three dimensions.

Sangar V, Lesk VI, Lesk AM.

Comput Biol Chem. 2008 Jun;32(3):212-4. doi: 10.1016/j.compbiolchem.2008.02.002. Epub 2008 Feb 12.

PMID:
18358782
21.

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. doi: 10.1093/bioinformatics/btm641. Epub 2008 Jan 5.

PMID:
18175768
22.

Quantitative sequence-function relationships in proteins based on gene ontology.

Sangar V, Blankenberg DJ, Altman N, Lesk AM.

BMC Bioinformatics. 2007 Aug 8;8:294.

23.

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
24.

MUSTANG: a multiple structural alignment algorithm.

Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM.

Proteins. 2006 Aug 15;64(3):559-74.

PMID:
16736488
25.

Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.

Zanuy D, Gunasekaran K, Lesk AM, Nussinov R.

J Mol Biol. 2006 Apr 21;358(1):330-45. Epub 2006 Feb 9.

PMID:
16503338
26.

What determines the spectrum of protein native state structures?

Lezon TR, Banavar JR, Lesk AM, Maritan A.

Proteins. 2006 May 1;63(2):273-7.

PMID:
16470841
27.

Molecular forces in antibody maturation.

Demirel MC, Lesk AM.

Phys Rev Lett. 2005 Nov 11;95(20):208106. Epub 2005 Nov 10.

PMID:
16384106
28.

Structural divergence and distant relationships in proteins: evolution of the globins.

Lecomte JT, Vuletich DA, Lesk AM.

Curr Opin Struct Biol. 2005 Jun;15(3):290-301. Review.

PMID:
15922591
29.

Functional insights from the distribution and role of homopeptide repeat-containing proteins.

Faux NG, Bottomley SP, Lesk AM, Irving JA, Morrison JR, de la Banda MG, Whisstock JC.

Genome Res. 2005 Apr;15(4):537-51.

30.

The high resolution crystal structure of a native thermostable serpin reveals the complex mechanism underpinning the stressed to relaxed transition.

Fulton KF, Buckle AM, Cabrita LD, Irving JA, Butcher RE, Smith I, Reeve S, Lesk AM, Bottomley SP, Rossjohn J, Whisstock JC.

J Biol Chem. 2005 Mar 4;280(9):8435-42. Epub 2004 Dec 7.

31.

Prediction of protein function from protein sequence and structure.

Whisstock JC, Lesk AM.

Q Rev Biophys. 2003 Aug;36(3):307-40. Review.

PMID:
15029827
32.

Hydrophobicity--getting into hot water.

Lesk AM.

Biophys Chem. 2003 Sep;105(2-3):179-82. Review.

PMID:
14499890
33.

Serpins in prokaryotes.

Irving JA, Steenbakkers PJ, Lesk AM, Op den Camp HJ, Pike RN, Whisstock JC.

Mol Biol Evol. 2002 Nov;19(11):1881-90.

PMID:
12411597
34.
36.

Modularity and homology: modelling of the titin type I modules and their interfaces.

Amodeo P, Fraternali F, Lesk AM, Pastore A.

J Mol Biol. 2001 Aug 10;311(2):283-96.

PMID:
11478861
37.

Protein structural alignments and functional genomics.

Irving JA, Whisstock JC, Lesk AM.

Proteins. 2001 Feb 15;42(3):378-82.

PMID:
11151008
38.
39.

Conformational changes in serpins: II. The mechanism of activation of antithrombin by heparin.

Whisstock JC, Pike RN, Jin L, Skinner R, Pei XY, Carrell RW, Lesk AM.

J Mol Biol. 2000 Sep 1;301(5):1287-305.

PMID:
10966821
40.

Antibody modeling: implications for engineering and design.

Morea V, Lesk AM, Tramontano A.

Methods. 2000 Mar;20(3):267-79. Review.

PMID:
10694450
41.

Conformational changes in serpins: I. The native and cleaved conformations of alpha(1)-antitrypsin.

Whisstock JC, Skinner R, Carrell RW, Lesk AM.

J Mol Biol. 2000 Feb 18;296(2):685-99.

PMID:
10669617
42.

Canonical structures for the hypervariable regions of T cell alphabeta receptors.

Al-Lazikani B, Lesk AM, Chothia C.

J Mol Biol. 2000 Jan 28;295(4):979-95.

PMID:
10656805
43.

Conformational changes in serpins: I. The native and cleaved conformations of alpha(1)-antitrypsin.

Whisstock JC, Skinner R, Carrell RW, Lesk AM.

J Mol Biol. 2000 Jan 21;295(3):651-65.

PMID:
10623554
44.

Tendamistat surface accessibility to the TEMPOL paramagnetic probe.

Scarselli M, Bernini A, Segoni C, Molinari H, Esposito G, Lesk AM, Laschi F, Temussi P, Niccolai N.

J Biomol NMR. 1999 Oct;15(2):125-33.

PMID:
10605086
45.
46.

Serpins in the Caenorhabditis elegans genome.

Whisstock JC, Irving JA, Bottomley SP, Pike RN, Lesk AM.

Proteins. 1999 Jul 1;36(1):31-41.

PMID:
10373004
47.

SH3 domains in prokaryotes.

Whisstock JC, Lesk AM.

Trends Biochem Sci. 1999 Apr;24(4):132-3. No abstract available.

PMID:
10322416
49.

An atlas of serpin conformations.

Whisstock J, Skinner R, Lesk AM.

Trends Biochem Sci. 1998 Feb;23(2):63-7. Review.

PMID:
9538691
50.

Antibody structure, prediction and redesign.

Morea V, Tramontano A, Rustici M, Chothia C, Lesk AM.

Biophys Chem. 1997 Oct;68(1-3):9-16.

PMID:
9468606

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