Arthur Lesk

Arthur Lesk

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Arthur Lesk

Arthur Lesk

Publications by authors named "Arthur Lesk"

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Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures.

Methods Mol Biol 2019 ;1958:123-131

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1007/978-1-4939-9161-7_6DOI Listing
July 2019

Statistical inference of protein structural alignments using information and compression.

Bioinformatics 2017 04;33(7):1005-1013

Faculty of Information Technology, Monash University, Clayton, VIC 3800, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btw757DOI Listing
April 2017

The Computational Analysis of Protein Structures: Sources, Methods, Systems and Results.

J Res Natl Inst Stand Technol 1989 Jan-Feb;94(1):85-92

European Molecular Biology Laboratory, Heidelberg, F.R.G.

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http://dx.doi.org/10.6028/jres.094.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4954598PMC
January 2017

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

J Comput Biol 2015 Jun 19;22(6):487-97. Epub 2015 Feb 19.

2The Huck Institute of Genomics, Proteomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania.

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http://dx.doi.org/10.1089/cmb.2014.0154DOI Listing
June 2015

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

Bioinformatics 2014 Sep;30(17):i512-8

Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://bioinformatics.oxfordjournals.org/content/30/17/i512.
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btu460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147913PMC
September 2014

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

Proteins 2014 Mar 18;82(3):349-53. Epub 2013 Oct 18.

Department of Biochemistry and Molecular Biology and The Huck Institute of Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania, 16802.

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http://dx.doi.org/10.1002/prot.24414DOI Listing
March 2014

How precise are reported protein coordinate data?

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

The Huck Institute of Genomics, Proteomics and Bioinformatics and the Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1107/S1399004713031787DOI Listing
March 2014

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

Authors:
Arthur M Lesk

Phys Life Rev 2013 Mar 26;10(1):33-4; discussion 39-40. Epub 2012 Oct 26.

Department of Biochemistry and Molecular Biology, and Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.plrev.2012.10.007DOI Listing
March 2013

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

Methods Mol Biol 2013 ;932:51-9

Clayton School of Information Technology, Monash University, Clayton, VIC, Australia.

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http://dx.doi.org/10.1007/978-1-62703-065-6_4DOI Listing
January 2013

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

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

Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia.

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http://dx.doi.org/10.1093/nar/gks436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394326PMC
July 2012

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

Bioinformatics 2012 Jun;28(12):i97-105

Clayton School of Information Technology, Monash University, Clayton VIC 3800, Australia.

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http://dx.doi.org/10.1093/bioinformatics/bts223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371855PMC
June 2012

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

Bioinformatics 2011 Jul;27(13):i43-51

Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117365PMC
July 2011

Cataloging topologies of protein folding patterns.

J Mol Recognit 2010 Mar-Apr;23(2):253-7

National ICT Australia Victoria Research Laboratory, The University of Melbourne, Victoria 3010, Australia.

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http://dx.doi.org/10.1002/jmr.1006DOI Listing
May 2010

Single and multiple input modules in regulatory networks.

Proteins 2008 Nov;73(2):320-4

The Huck Institute for Genomics, Proteomics, and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1002/prot.22053DOI Listing
November 2008

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

BMC Syst Biol 2008 Aug 12;2:73. Epub 2008 Aug 12.

The Huck Institute for Genomics, Proteomics, and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/1752-0509-2-73DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538512PMC
August 2008

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

Comput Biol Chem 2008 Jun 12;32(3):212-4. Epub 2008 Feb 12.

Department of Biochemistry and Molecular Biology, and the Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S147692710800006
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http://dx.doi.org/10.1016/j.compbiolchem.2008.02.002DOI Listing
June 2008

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

Protein Sci 2008 May 27;17(5):918-29. Epub 2008 Mar 27.

International School for Advanced Studies and CNR-INFM Democritos, 34014 Trieste, Italy.

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http://doi.wiley.com/10.1110/ps.073390208
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http://dx.doi.org/10.1110/ps.073390208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2327282PMC
May 2008

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

Bioinformatics 2008 Mar 5;24(5):645-51. Epub 2008 Jan 5.

Department of Biochemistry and Molecular Biology and The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm641DOI Listing
March 2008

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

BMC Bioinformatics 2007 Aug 8;8:294. Epub 2007 Aug 8.

Department of Biochemistry and Molecular Biology, Center of Computational Biology and Genomics, The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-8-294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976327PMC
August 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

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

Proteins 2007 Mar;66(4):869-76

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1002/prot.21241DOI Listing
March 2007

MUSTANG: a multiple structural alignment algorithm.

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

Department of Computer Science and Software Engineering, The University of Melbourne, Parkville, Melbourne, Victoria, 3010 Australia.

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http://doi.wiley.com/10.1002/prot.20921
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http://dx.doi.org/10.1002/prot.20921DOI Listing
August 2006

What determines the spectrum of protein native state structures?

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

Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1002/prot.20869DOI Listing
May 2006

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

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

Department of Chemical Engineering, E.T.S.E.I.B.-U.P.C., Av. Diagonal 647, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1016/j.jmb.2006.01.070DOI Listing
April 2006

Molecular forces in antibody maturation.

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

College of Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1103/PhysRevLett.95.208106DOI Listing
November 2005

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

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

Department of Chemistry, The Huck Institutes of the Life Sciences: Genomics, Proteomics and Bioinformatics Institute, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.sbi.2005.05.008DOI Listing
June 2005

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

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

Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Computer Science and Software Engineering, Monash University, Clayton Campus, Melbourne, VIC 3800, Australia.

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http://www.genome.org/cgi/doi/10.1101/gr.3096505
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http://dx.doi.org/10.1101/gr.3096505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1074368PMC
April 2005

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

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

Protein Crystallography Unit, Monash Centre for Synchrotron Science, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Victorian Bioinformatics Consortium, P. O. Box 53, Australia.

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http://dx.doi.org/10.1074/jbc.M410206200DOI Listing
March 2005

Hydrophobicity--getting into hot water.

Authors:
Arthur M Lesk

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

Department of Haematology, University of Cambridge Clinical School, Wellcome Trust/MRC Building, Hills Road, CB2 2XY, Cambridge, UK.

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http://dx.doi.org/10.1016/s0301-4622(03)00086-3DOI Listing
September 2003

Prediction of protein function from protein sequence and structure.

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

Department of Biochemistry and Molecular Biology, Victorian Bioinformatics Consortium, Monash University, Clayton Campus, ARC Centre for Structural and Functional Microbial Genetics, Victoria, Australia.

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http://dx.doi.org/10.1017/s0033583503003901DOI Listing
August 2003

A cluster of familial Creutzfeldt-Jakob disease mutations recapitulate conserved residues in Doppel: a case of molecular mimicry?

FEBS Lett 2002 Dec;532(1-2):21-6

Centre for Research in Neurodegenerative Diseases, University of Toronto, Tanz Neuroscience Building, 6 Queen's Park Crescent West, Toronto, ON, Canada M5S 3H2.

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http://dx.doi.org/10.1016/s0014-5793(02)03614-1DOI Listing
December 2002

Serpins in prokaryotes.

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

Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1093/oxfordjournals.molbev.a004012DOI Listing
November 2002

Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.

Mol Biol Evol 2002 Oct;19(10):1645-55

Department of Molecular Biology, Princeton University, New Jersey 08544, USA.

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http://dx.doi.org/10.1093/oxfordjournals.molbev.a003988DOI Listing
October 2002