Works by Thornton, Janet M.

Results: 148

Domain-ligand mapping for enzymes.

Published in:

Journal of Molecular Recognition, 2010, v. 23, n. 2, p. 194, doi. 10.1002/jmr.992

By:

Bashton, Matthew;
Thornton, Janet M

Publication type:

Article

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1753-9

By:

Martin-Herranz, Daniel E.;
Aref-Eshghi, Erfan;
Bonder, Marc Jan;
Stubbs, Thomas M.;
Choufani, Sanaa;
Weksberg, Rosanna;
Stegle, Oliver;
Sadikovic, Bekim;
Reik, Wolf;
Thornton, Janet M.

Publication type:

Article

Ligand selectivity and competition between enzymes in silico.

Published in:

Nature Biotechnology, 2004, v. 22, n. 8, p. 1039, doi. 10.1038/nbt999

By:

Macchiarulo, Antonio;
Nobeli, Irene;
Thornton, Janet M

Publication type:

Article

The CATH protein family database: A resource for structural and functional annotation of genomes.

Published in:

Proteomics, 2002, v. 2, n. 1, p. 11, doi. 10.1002/1615-9861(200201)2:1<11::AID-PROT11>3.0.CO;2-T

By:

Orengo, Christine A.;
Bray, James E.;
Buchan, Daniel W. A.;
Harrison, Andrew;
Lee, David;
Pearl, Frances M. G.;
Sillitoe, Ian;
Todd, Annabel E.;
Thornton, Janet M.

Publication type:

Article

Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA).

Published in:

Journal of Molecular Evolution, 2006, v. 63, n. 4, p. 513, doi. 10.1007/s00239-005-0289-7

By:

Ranea, Juan A. G.;
Sillero, Antonio;
Thornton, Janet M.;
Orengo, Christine A.

Publication type:

Article

Srinivasan (1962–2021) in Bioinformatics and beyond.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2377, doi. 10.1093/bioinformatics/btac054

By:

Gromiha, M Michael;
Orengo, Christine A;
Sowdhamini, Ramanathan;
Thornton, and Janet M

Publication type:

Article

GRaSP: a graph-based residue neighborhood strategy to predict binding sites.

Published in:

Bioinformatics, 2020, v. 36, p. i726, doi. 10.1093/bioinformatics/btaa805

By:

Santana, Charles A;
Silveira, Sabrina de A;
Moraes, João P A;
Izidoro, Sandro C;
Melo-Minardi, Raquel C de;
Ribeiro, António J M;
Tyzack, Jonathan D;
Borkakoti, Neera;
Thornton, Janet M

Publication type:

Article

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

Published in:

Nucleic Acids Research, 2013, v. 41, p. D490, doi. 10.1093/nar/gks1211

By:

Sillitoe, Ian;
Cuff, Alison L.;
Dessailly, Benoit H.;
Dawson, Natalie L.;
Furnham, Nicholas;
David Lee;
Lees, Jonathan G.;
Lewis, Tony E.;
Studer, Romain A.;
Rentzsch, Robert;
Yeats, Corin;
Thornton, Janet M.;
Orengo, Christine A.

Publication type:

Article

The EBI enzyme portal.

Published in:

Nucleic Acids Research, 2013, v. 41, p. D773, doi. 10.1093/nar/gks1112

By:

Alcántara, Rafael;
Onwubiko, Joseph;
Hong Cao;
de Matos, Paula;
Cham, Jennifer A.;
Jacobsen, Jules;
Holliday, Gemma L.;
Fischer, Julia D.;
Rahman, Syed Asad;
Jassal, Bijay;
Goujon, Mikael;
Rowland, Francis;
Velankar, Sameer;
López, Rodrigo;
Overington, John P.;
Kleywegt, Gerard J.;
Hermjakob, Henning;
O'Donovan, Claire;
Martín, María Jesús;
Thornton, Janet M.

Publication type:

Article

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.

Published in:

Nucleic Acids Research, 2012, p. D776, doi. 10.1093/nar/gkr852

By:

Furnham, Nicholas;
Sillitoe, Ian;
Holliday, Gemma L.;
Cuff, Alison L.;
Rahman, Syed A.;
Laskowski, Roman A.;
Orengo, Christine A.;
Thornton, Janet M.

Publication type:

Article

PROCOGNATE: a cognate ligand domain mapping for enzymes.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D618

By:

Bashton, Matthew;
Nobeli, Irene;
Thornton, Janet M.

Publication type:

Article

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.

Published in:

Nucleic Acids Research, 2007, v. 35, p. d291, doi. 10.1093/nar/gkl959

By:

Greene, Lesley H.;
Lewis, Tony E.;
Addou, Sarah;
Cuff, Alison;
Dallman, Tim;
Dibley, Mark;
Redfern, Oliver;
Pearl, Frances;
Nambudiry, Rekha;
Reid, Adam;
Sillitoe, Ian;
Yeats, Corin;
Thornton, Janet M.;
Orengo, Christine A.

Publication type:

Article

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.

Published in:

Nucleic Acids Research, 2007, v. 35, p. d515, doi. 10.1093/nar/gkl774

By:

Holliday, Gemma L.;
Almonacid, Daniel E.;
Bartlett, Gail J.;
O'Boyle, Noel M.;
Torrance, James W.;
Murray-Rust, Peter;
Mitchell, John B. O.;
Thornton, Janet M.

Publication type:

Article

ProFunc: a server for predicting protein function from 3D structure.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 2, p. w89, doi. 10.1093/nar/gki414

By:

Laskowski, Roman A.;
Watson, James D.;
Thornton, Janet M.

Publication type:

Article

Detecting DNA-binding helix–turn–helix structural motifs using sequence and structure information.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 7, p. 2129, doi. 10.1093/nar/gki349

By:

Pellegrini-Calace, Marialuisa;
Thornton, Janet M.

Publication type:

Article

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d266

By:

Laskowski, Roman A.;
Chistyakov, Victor V.;
Thornton, Janet M.

Publication type:

Article

Identifying DNA-binding proteins using structural motifs and the electrostatic potential.

Published in:

Nucleic Acids Research, 2004, v. 32, n. 16, p. 4732, doi. 10.1093/nar/gkh803

By:

Shanahan, Hugh P.;
Garcia, Mario A.;
Jones, Susan;
Thornton, Janet M.

Publication type:

Article

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d129

By:

Porter, Craig T.;
Bartlett, Gail J.;
Thornton, Janet M.

Publication type:

Article

Using electrostatic potentials to predict DNA‐binding sites on DNA‐binding proteins.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 24, p. 7189, doi. 10.1093/nar/gkg922

By:

Jones, Susan;
Shanahan, Hugh P.;
Berman, Helen M.;
Thornton, Janet M.

Publication type:

Article

Using structural motif templates to identify proteins with DNA binding function.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 11, p. 2811, doi. 10.1093/nar/gkg386

By:

Jones, Susan;
Barker, Jonathan A.;
Nobeli, Irene;
Thornton, Janet M.

Publication type:

Article

Gene3D: structural assignments for the biologist and bioinformaticist alike.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 1, p. 469, doi. 10.1093/nar/gkg051

By:

Buchan, Daniel W. A.;
Rison, Stuart C. G.;
Bray, James E.;
Lee, David;
Pearl, Frances;
Thornton, Janet M.;
Orengo, Christine A.

Publication type:

Article

On the molecular discrimination between adenine and guanine by proteins.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 21, p. 4294, doi. 10.1093/nar/29.21.4294

By:

Nobeli, Irene;
Laskowski, Roman A.;
Valdar, William S. J.;
Thornton, Janet M.

Publication type:

Article

Amino acid–base interactions: a three-dimensional analysis of protein–DNA interactions at an atomic level.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 13, p. 2860, doi. 10.1093/nar/29.13.2860

By:

Luscombe, Nicholas M.;
Laskowski, Roman A.;
Thornton, Janet M.

Publication type:

Article

Protein–RNA interactions: a structural analysis.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 4, p. 943, doi. 10.1093/nar/29.4.943

By:

Jones, Susan;
Daley, David T. A.;
Luscombe, Nicholas M.;
Berman, Helen M.;
Thornton, Janet M.

Publication type:

Article

A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data.

Published in:

PLoS ONE, 2020, v. 15, n. 10, p. 1, doi. 10.1371/journal.pone.0240824

By:

Ivanov, Dobril K.;
Bostelmann, Gerrit;
Lan-Leung, Benoit;
Williams, Julie;
Partridge, Linda;
Escott-Price, Valentina;
Thornton, Janet M.

Publication type:

Article

A method for localizing ligand binding pockets in protein structures.

Published in:

Proteins, 2006, v. 62, n. 2, p. 479, doi. 10.1002/prot.20769

By:

Glaser, Fabian;
Morris, Richard J.;
Najmanovich, Rafael J.;
Laskowski, Roman A.;
Thornton, Janet M.

Publication type:

Article

Toward the detection and validation of repeats in protein structure.

Published in:

Proteins, 2004, v. 57, n. 2, p. 365, doi. 10.1002/prot.20202

By:

Murray, Kevin B.;
Taylor, William R.;
Thornton, Janet M.

Publication type:

Article

A template search reveals mechanistic similarities and differences in β-ketoacyl synthases (KAS) and related enzymes.

Published in:

Proteins, 2003, v. 52, n. 3, p. 427, doi. 10.1002/prot.10421

By:

Jennifer H. Dawe;
Craig T. Porter;
Janet M. Thornton;
Alethea B. Tabor

Publication type:

Article

A novel approach to the recognition of protein architecture from sequence using fourier analysis and neural networks.

Published in:

Proteins, 2003, v. 50, n. 2, p. 290, doi. 10.1002/prot.10290

By:

Shepherd, Adrian J.;
Gorse, Denise;
Thornton, Janet M.

Publication type:

Article

Prediction of strand pairing in antiparallel and parallel β-sheets using information theory.

Published in:

Proteins, 2002, v. 48, n. 2, p. 178, doi. 10.1002/prot.10152

By:

Steward, Robert E.;
Thornton, Janet M.

Publication type:

Article

Protein-protein interfaces: Analysis of amino acid conservation in homodimers.

Published in:

Proteins, 2001, v. 42, n. 1, p. 108, doi. 10.1002/1097-0134(20010101)42:1<108::AID-PROT110>3.0.CO;2-O

By:

Valdar, William S. J.;
Thornton, Janet M.

Publication type:

Article

Discriminating between homodimeric and monomeric proteins in the crystalline state.

Published in:

Proteins, 2000, v. 41, n. 1, p. 47, doi. 10.1002/1097-0134(20001001)41:1<47::AID-PROT80>3.0.CO;2-8

By:

Ponstingl, Hannes;
Henrick, Kim;
Thornton, Janet M.

Publication type:

Article

<sup>1</sup>H NMR structure of an antifungal γ-thionin protein SIα1: Similarity to scorpion toxins.

Published in:

Proteins, 1998, v. 32, n. 3, p. 334, doi. 10.1002/(SICI)1097-0134(19980815)32:3<334::AID-PROT9>3.0.CO;2-H

By:

Bloch, Carlos;
Patel, Sunil U.;
Baud, Franck;
Zvelebil, Marketa J.J.M.;
Carr, Mark D.;
Sadler, Peter J.;
Thornton, Janet M.

Publication type:

Article

Non-randomness in side-chain packing: the distribution of interplanar angles.

Published in:

Proteins, 1997, v. 29, n. 3, p. 370, doi. 10.1002/(SICI)1097-0134(199711)29:3<370::AID-PROT10>3.0.CO;2-K

By:

Mitchell, John B.O.;
Laskowski, Roman A.;
Thornton, Janet M.

Publication type:

Article

Assessment of comparative modeling in CASP2.

Published in:

Proteins, 1997, v. 29, n. S1, p. 14, doi. 10.1002/(SICI)1097-0134(1997)1+<14::AID-PROT4>3.0.CO;2-O

By:

Martin, Andrew C. R.;
MacArthur, Malcolm W.;
Thornton, Janet M.

Publication type:

Article

Towards meeting the paracelsus challenge: The design, synthesis, and characterization of paracelsin-43, an α-helical protein with over 50% sequence identity to an all-β protein.

Published in:

Proteins, 1996, v. 24, n. 4, p. 502, doi. 10.1002/(SICI)1097-0134(199604)24:4<502::AID-PROT9>3.0.CO;2-F

By:

Jones, David T.;
Moody, Claire M.;
Uppenbrink, Julia;
Viles, John H.;
Doyle, Paul M.;
Harris, C. John;
Pearl, Laurence H.;
Sadler, Peter J.;
Thornton, Janet M.

Publication type:

Article

Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.

Published in:

Proteins, 1995, v. 23, n. 3, p. 387, doi. 10.1002/prot.340230312

By:

Jones, David T.;
Miller, Robert T.;
Thornton, Janet M.

Publication type:

Article

Conformational analysis of protein structures derived from NMR data.

Published in:

Proteins, 1993, v. 17, n. 3, p. 232, doi. 10.1002/prot.340170303

By:

MacArthur, Malcolm W.;
Thornton, Janet M.

Publication type:

Article

Stereochemical quality of protein structure coordinates.

Published in:

Proteins, 1992, v. 12, n. 4, p. 345, doi. 10.1002/prot.340120407

By:

Morris, Anne Louise;
MacArthur, Malcolm W.;
Hutchinson, E. Gail;
Thornton, Janet M.

Publication type:

Article

HERA-A program to draw schematic diagrams of protein secondary structures.

Published in:

Proteins, 1990, v. 8, n. 3, p. 203, doi. 10.1002/prot.340080303

By:

Hutchinson, E. Gail;
Thornton, Janet M.

Publication type:

Article

Rebuilding flavodoxin from Cα coordinates: A test study.

Published in:

Proteins, 1989, v. 5, n. 2, p. 170, doi. 10.1002/prot.340050212

By:

Reid, Lorne S.;
Thornton, Janet M.

Publication type:

Article

Peptide–protein interactions: an overview.

Published in:

Quarterly Reviews of Biophysics, 1993, v. 26, n. 3, p. 333, doi. 10.1017/S0033583500002870

By:

Zvelebil, Markéta J. J. M.;
Thornton, Janet M.

Publication type:

Article

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.

Published in:

FEBS Journal, 2011, v. 278, n. 20, p. 3835, doi. 10.1111/j.1742-4658.2011.08190.x

By:

Holliday, Gemma L.;
Fischer, Julia D.;
Mitchell, John B. O.;
Thornton, Janet M.

Publication type:

Article

DAF-16/FoxO Directly Regulates an Atypical AMP-Activated Protein Kinase Gamma Isoform to Mediate the Effects of Insulin/IGF-1 Signaling on Aging in <i>Caenorhabditis elegans</i>.

Published in:

PLoS Genetics, 2014, v. 10, n. 2, p. 1, doi. 10.1371/journal.pgen.1004109

By:

Tullet, Jennifer M. A.;
Araiz, Caroline;
Sanders, Matthew J.;
Au, Catherine;
Benedetto, Alexandre;
Papatheodorou, Irene;
Clark, Emily;
Schmeisser, Kathrin;
Jones, Daniel;
Schuster, Eugene F.;
Thornton, Janet M.;
Gems, David

Publication type:

Article

Regulation of Lifespan, Metabolism, and Stress Responses by the Drosophila SH2B Protein, Lnk.

Published in:

PLoS Genetics, 2010, v. 6, n. 3, p. 1, doi. 10.1371/journal.pgen.1000881

By:

Slack, Cathy;
Werz, Christian;
Wieser, Daniela;
Alic, Nazif;
Foley, Andrea;
Stocker, Hugo;
Withers, Dominic J.;
Thornton, Janet M.;
Hafen, Ernst;
Partridge, Linda

Publication type:

Article

Prediction of protein structure from amino acid sequence.

Published in:

Nature, 1978, v. 271, n. 5640, p. 15, doi. 10.1038/271015a0

By:

Sternberg, Michael J. E.;
Thornton, Janet M.

Publication type:

Article

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.

Published in:

Bioinformatics, 2007, v. 23, n. 2, p. e104

By:

Rafael J. Najmanovich;
Abdellah Allali-Hassani;
Richard J. Morris;
Ludmila Dombrovsky;
Patricia W. Pan;
Masoud Vedadi;
Alexander N. Plotnikov;
Aled Edwards;
Cheryl Arrowsmith;
Janet M. Thornton

Publication type:

Article

MACiE: a database of enzyme reaction mechanisms.

Published in:

Bioinformatics, 2005, v. 21, n. 23, p. 4315, doi. 10.1093/bioinformatics/bti693

By:

Gemma L. Holliday;
Gail J. Bartlett;
Daniel E. Almonacid;
Noel M. O'Boyle;
Peter Murray-Rust;
Janet M. Thornton;
John B. O. Mitchell

Publication type:

Article

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.

Published in:

Bioinformatics, 2005, v. 21, n. 10, p. 2347

By:

Janet M. Thornton

Publication type:

Article

A practical and robust sequence search strategy for structural genomics target selection.

Published in:

Bioinformatics, 2004, v. 20, n. 14, p. 2288, doi. 10.1093/bioinformatics/bth240

By:

James E. Bray;
Russell L. Marsden;
Stuart C.G. Rison;
Alexei Savchenko;
Aled M. Edwards;
Janet M. Thornton;
Christine A. Orengo

Publication type:

Article