Janet M. Thornton

发表

A rapid classification protocol for the CATH Domain Database to support structural genomics

James E. Bray, Frances M. G. Pearl, Nigel J. Martin, 2001, Nucleic Acids Res..

Protein Engineering '87—conference report

Janet M. Thornton, Michael J. Gait, Ronald Wetzel, 1987 .

Case Studies: Function Predictions of Structural Genomics Results

Janet M. Thornton, James D. Watson, J. Thornton, 2009 .

Metal-MACiE: a database of metals involved in biological catalysis

Janet M. Thornton, Gemma L. Holliday, Gabriele Cavallaro, 2009, Bioinform..

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity

Janet M. Thornton, Nicholas Furnham, Nidhi Tyagi, 2015, PLoS Comput. Biol..

PDBsum additions

Karel Berka, Janet M. Thornton, Roman A. Laskowski, 2013, Nucleic Acids Res..

Faculty Opinions recommendation of A simple physical model for the prediction and design of protein-DNA interactions.

Janet M. Thornton, J. Thornton, 2004 .

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

Janet M. Thornton, Rafael Najmanovich, Richard J. Morris, 2007, Bioinform..

Software engineering challenges in bioinformatics

Janet M. Thornton, Jonathan A. Barker, J. Thornton, 2004, Proceedings. 26th International Conference on Software Engineering.

ISMB/ECCB 2004 Organization

David R. Gilbert, Catherine Brooksbank, Janet M. Thornton, 2004, ISMB/ECCB.

ELIXIR - A European Infrastructure for Biological Information: Challenges and Progress

Janet M. Thornton, J. Thornton, 2009, GI Jahrestagung.

Faculty Opinions recommendation of A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.

Janet M. Thornton, J. Thornton, 2003 .

CATH: expanding the horizons of structure-based functional annotations for genome sequences

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2018, Nucleic Acids Res..

Faculty Opinions recommendation of A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology.

Janet M. Thornton, J. Thornton, 2004 .

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif

Janet M. Thornton, Carles Ferrer-Costa, Hugh P. Shanahan, 2005, Bioinform..

Gene3D: structural assignments for the biologist and bioinformaticist alike

James E. Bray, Frances M. G. Pearl, Daniel W. A. Buchan, 2003, Nucleic Acids Res..

PROCOGNATE: a cognate ligand domain mapping for enzymes

Janet M. Thornton, Irene Nobeli, Matthew Bashton, 2007, Nucleic Acids Res..

CATH: comprehensive structural and functional annotations for genome sequences

David A. Lee, Ian Sillitoe, Janet M. Thornton, 2014, Nucleic Acids Res..

Transform-MinER: transforming molecules in enzyme reactions

Neera Borkakoti, Janet M. Thornton, Jonathan D. Tyzack, 2018, Bioinform..

Insights into protein evolution and function from the CATH structural database

James E. Bray, Frances M. G. Pearl, David A. Lee, 2001 .

An examination of the conservation of surface patch polarity for proteins

Janet M. Thornton, Hugh P. Shanahan, J. Thornton, 2004, Bioinform..

BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential

Janet M. Thornton, John B. O. Mitchell, Roman A. Laskowski, 1999, J. Comput. Chem..

David R. Gilbert, Catherine Brooksbank, Janet M. Thornton, 2004, ISMB/ECCB.

Towards automated structure-based identification of protein ligands

Janet M. Thornton, Roman A. Laskowski, Marian Novotny, 2007 .

Recognizing the fold of a protein structure

Frances M. G. Pearl, Andrew P. Harrison, Ian Sillitoe, 2003, Bioinform..

An automated protocol for modelling peptide substrates to proteases

Janet M. Thornton, Rodrigo Ochoa, Pilar Cossio, 2020, BMC Bioinformatics.

Variation of geometrical and physicochemical properties in protein binding pockets and their ligands

Janet M. Thornton, Roman A. Laskowski, Richard J. Morris, 2007, BMC Bioinformatics.

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

Janet M. Thornton, Craig T. Porter, Gail J. Bartlett, 2004, Nucleic Acids Res..

BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data

Janet M. Thornton, Mark J. Forster, John B. O. Mitchell, 1999, J. Comput. Chem..

The European Bioinformatics Institute’s data resources

Catherine Brooksbank, Janet M. Thornton, Graham Cameron, 2009, Nucleic Acids Res..

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

Nicholas M. Luscombe, Janet M. Thornton, Roman A. Laskowski, 2001, Nucleic Acids Res..

Coordination of structural bioinformatics activities across Europe

Sameer Velankar, Shoshana J. Wodak, Janet M. Thornton, 2018, Acta Crystallographica Section A: Foundations and Advances.

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing

Irene Papatheodorou, Janet M. Thornton, Rudolfs Petrovs, 2014, Bioinform..

The EBI enzyme portal

Christoph Steinbeck, Maria Jesus Martin, Claire O'Donovan, 2012, Nucleic Acids Res..

PROCHECK: validation of protein‐structure coordinates

Janet M. Thornton, Roman A. Laskowski, Malcolm W. MacArthur, 2012 .

Motif-based searching in TOPS protein topology databases

David R. Gilbert, Janet M. Thornton, David R. Westhead, 1999, Bioinform..

Reaction Decoder Tool (RDT): extracting features from chemical reactions

Christoph Steinbeck, Janet M. Thornton, Gemma L. Holliday, 2016, Bioinform..

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

Janet M. Thornton, Nicholas Furnham, Gemma L. Holliday, 2017, Nucleic Acids Res..

The Protein Feature Ontology: a tool for the unification of protein feature annotations

Andreas Prlic, Karen Eilbeck, Claire O'Donovan, 2008, Bioinform..

The proteome and the metabolome

Janet M. Thornton, 2003, ECCB.

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

James E. Bray, Janet M. Thornton, Christine A. Orengo, 2004, Bioinform..

The European Bioinformatics Institute's data resources: towards systems biology

Catherine Brooksbank, Janet M. Thornton, Graham Cameron, 2004, Nucleic Acids Res..

Faculty Opinions recommendation of Calmodulin target database.

Janet M. Thornton, J. Thornton, 2003 .

Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset

Janet M. Thornton, Nick Goldman, Roman A. Laskowski, 2013, PLoS Comput. Biol..

Living longer by dieting: analysis of transcriptional response after caloric restriction

Janet M. Thornton, Linda Partridge, Dominic J. Withers, 2005, BMC Bioinformatics.

Programs and program systems in wide use

Randy J. Read, Paul D. Adams, Anastassis Perrakis, 2006 .

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites

Janet M. Thornton, Rafael Najmanovich, Natalja Kurbatova, 2008, ECCB.

MACiE: a database of enzyme reaction mechanisms

Peter Murray-Rust, Janet M. Thornton, Gemma L. Holliday, 2005, Bioinform..

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

Janet M. Thornton, James D. Watson, Roman A. Laskowski, 2005, Nucleic Acids Res..

The CATH database: an extended protein family resource for structural and functional genomics

James E. Bray, Frances M. G. Pearl, Nigel J. Martin, 2003, Nucleic Acids Res..

PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure

Janet M. Thornton, Marialuisa Pellegrini-Calace, Tim Maiwald, 2009, PLoS Comput. Biol..

Evolutionary Models for Formation of Network Motifs and Modularity in the Saccharomyces Transcription Factor Network

Janet M. Thornton, Jonathan J. Ward, J. Thornton, 2007, PLoS Comput. Biol..

Software Tools for Protein Structure Analysis and Fold Classification

Janet M. Thornton, Christine A. Orengo, Roman A. Laskowski, 1999 .

Microeconomic Principles Explain an Optimal Genome Size in Bacteria

Janet M. Thornton, Christine A. Orengo, Juan Garcia Ranea, 2004, Spanish Bioinformatics Conference.

Lessons from analyzing protein structures

Janet M. Thornton, J. Thornton, 1992 .

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

Janet M. Thornton, Nicholas Furnham, Julius O. B. Jacobsen, 2013, Nucleic Acids Res..

The CATH Database provides insights into protein structure/function relationships

James E. Bray, Frances M. G. Pearl, Annabel E. Todd, 1999, Nucleic Acids Res..

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data

Stijn van Dongen, Anton J. Enright, Tom C. Freeman, 2007, PLoS Comput. Biol..

Faculty Opinions recommendation of Computational comparison of two mouse draft genomes and the human golden path.

Janet M. Thornton, J. Thornton, 2003 .

The rapid generation of mutation data matrices from protein sequences

William R. Taylor, Janet M. Thornton, David T. Jones, 1992, Comput. Appl. Biosci..

Small Molecule Subgraph Detector (SMSD) toolkit

Rainer Schrader, Janet M. Thornton, Gemma L. Holliday, 2009, J. Cheminformatics.

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2010, Nucleic Acids Res..

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

Peter Murray-Rust, Janet M. Thornton, Gemma L. Holliday, 2006, Nucleic Acids Res..

PROTEIN FOLD FAMILIES AND STRUCTURAL MOTIFS

William R. Taylor, Janet M. Thornton, Christine A. Orengo, 1994 .

The European Bioinformatics Institute’s data resources 2014

Rolf Apweiler, Catherine Brooksbank, Janet M. Thornton, 2013, Nucleic Acids Res..

A public regulator of longevity acts via lineage-specific effectors.

Janet M. Thornton, Dominic J. Withers, Eric Blanc, 2006 .

Building and design

Janet M. Thornton, 1987, Nature.

Faculty Opinions recommendation of Apollo: a sequence annotation editor.

Janet M. Thornton, J. Thornton, 2003 .

Mapping Human Metabolic Pathways in the Small Molecule Chemical Space

Janet M. Thornton, Irene Nobeli, Antonio Macchiarulo, 2009, J. Chem. Inf. Model..

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Arne Elofsson, Matthias Rarey, Anastassis Perrakis, 2020, F1000Research.

Protein domain superfolds and superfamilies

Janet M. Thornton, Christine A. Orengo, David T. Jones, 1994 .

Une technique déclarative pour filtrer des motifs topologiques de protéines

David R. Gilbert, Janet M. Thornton, David R. Westhead, 2000, Journées Francophones de Programmation Logique par Contraintes.

A Computer System to Perform Structure Comparison using Representations of Protein Structure

David R. Gilbert, Janet M. Thornton, David R. Westhead, 2002, Comput. Chem..

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

David A. Lee, Ian Sillitoe, Janet M. Thornton, 2012, Nucleic Acids Res..

The Impact of Structural Proteomics on Macromolecular Structure Databases

Janet M. Thornton, James D. Watson, J. Thornton, 2008 .

[Invited Lecture] Protein Folds and Functions

Janet M. Thornton, Christine A. Orengo, Roman A. Laskowski, 1998, German Conference on Bioinformatics.

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

Mona Singh, Thomas A. Funkhouser, Janet M. Thornton, 2009, PLoS Comput. Biol..

Protein folds and their recognition from sequence

Janet M. Thornton, Christine A. Orengo, David T. Jones, 1996 .

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

Janet M. Thornton, Roman A. Laskowski, Victor V. Chistyakov, 2004, Nucleic Acids Res..

Evaluation of a knowledge‐based potential of mean force for scoring docked protein–ligand complexes

Janet M. Thornton, John B. O. Mitchell, Irene Nobeli, 2001, J. Comput. Chem..

Faculty Opinions recommendation of Enzyme family classification by support vector machines.

Janet M. Thornton, J. Thornton, 2004 .

The CoFactor database: organic cofactors in enzyme catalysis

Janet M. Thornton, Gemma L. Holliday, Julia D. Fischer, 2010, Bioinform..

Sequences and topology.

Mark Gerstein, Janet M. Thornton, M. Gerstein, 2001, Current opinion in structural biology.

The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2008, Nucleic Acids Res..

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins

Janet M. Thornton, Romina Oliva, Marialuisa Pellegrini-Calace, 2009, Bioinform..

Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania

Ian H. Gilbert, Janet M. Thornton, Roman A. Laskowski, 1998, J. Comput. Aided Mol. Des..

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

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2011, Nucleic Acids Res..

From protein structure to biochemical function?

Janet M. Thornton, James D. Watson, Roman A. Laskowski, 2004, Journal of Structural and Functional Genomics.

Methods to characterize the structure of enzyme binding sites

Janet M. Thornton, Abdullah Kahraman, J. Thornton, 2008 .

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis

Janet M. Thornton, Jonathan A. Barker, J. Thornton, 2003, Bioinform..

SCOPEC: a database of protein catalytic domains

Janet M. Thornton, Richard A. George, Bissan Al-Lazikani, 2004, ISMB/ECCB.

Analysis and modelling of antibodies.

Janet M. Thornton, Acr Martin, Rm MacCallum, 1995 .

Bridging cheminformatics and bioinformatics by using protein structures.

Janet M. Thornton, Awe Chan, Roman A. Laskowski, 2001 .

Macromolecular structure information and databases

Christopher J. Rawlings, Shoshana J. Wodak, Jean Richelle, 1996 .

Delivering ICT infrastructure for biomedical research

Tommi H. Nyrönen, Per Öster, Janet M. Thornton, 2012, WICSA/ECSA '12.

SurvCurv database and online survival analysis platform update

Janet M. Thornton, Linda Partridge, Matthias Ziehm, 2015, Bioinform..

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

Frances M. G. Pearl, Andrew P. Harrison, David A. Lee, 2004, Nucleic Acids Res..

Protein fold recognition

Janet M. Thornton, David T. Jones, David T. Jones, 1993, J. Comput. Aided Mol. Des..

A rapid algorithm for generating minimal pathway distances

Lazaros G. Papageorgiou, Janet M. Thornton, Idl Bogle, 2001, Intelligent Systems in Molecular Biology.

Structure‐Based Prediction of Enzymes and Their Active Sites

Janet M. Thornton, James Torrance, James W. Torrance, 2008 .

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

Frances M. G. Pearl, Ian Sillitoe, Janet M. Thornton, 2006, Nucleic Acids Res..

EuroQSAR 2002: Designing Drugs and Crop Protectants: processes, problems and solution

Janet M. Thornton, Irene Nobeli, J. Thornton, 2003 .

Faculty Opinions recommendation of Building an automated classification of DNA-binding protein domains.

Janet M. Thornton, J. Thornton, 2002 .

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

Janet M. Thornton, Roman A. Laskowski, A. W. Edith Chan, 2013, Acta crystallographica. Section D, Biological crystallography.

Faculty Opinions recommendation of Sputnik: a database platform for comparative plant genomics.

Janet M. Thornton, J. Thornton, 2003 .

The European Bioinformatics Institute: Leading the bioinformatics revolution

Janet M. Thornton, Graham Cameron, Cath Brooksbank, 2004 .

Assigning genomic sequences to CATH

James E. Bray, Frances M. G. Pearl, Andrew P. Harrison, 2000, Nucleic Acids Res..

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2012, PLoS Comput. Biol..

WSsas: a web service for the annotation of functional residues through structural homologues

Janet M. Thornton, Roman A. Laskowski, David Talavera, 2009, Bioinform..

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

Janet M. Thornton, Rafael Najmanovich, Richard J. Morris, 2005, Bioinform..

Structural survey

Janet M. Thornton, J. Thornton, 1987, Nature.

Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy

Janet M. Thornton, Roman A. Laskowski, Malcolm W. MacArthur, 1994 .

Editorial overviewSequences and topology

Mark Gerstein, Janet M. Thornton, 2003 .

Prediction of progress at last

Janet M. Thornton, T. P. Flores, David T. Jones, 1991, Nature.

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

Janet M. Thornton, Bekim Sadikovic, Sanaa Choufani, 2019, Genome Biology.

BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential

Janet M. Thornton, John B. O. Mitchell, Roman A. Laskowski, 1999 .

Metal ions in biological catalysis: from enzyme databases to general principles

Janet M. Thornton, Gemma L. Holliday, Ivano Bertini, 2008, JBIC Journal of Biological Inorganic Chemistry.

Protein–DNA Interactions: The Story so Far and a New Method for Prediction

Janet M. Thornton, Susan Jones, J. Thornton, 2003, Comparative and Functional Genomics.

Prediction of protein structure from amino acid sequence

Janet M. Thornton, Michael J. E. Sternberg, M. Sternberg, 1978, Nature.

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster † †Electronic supplementary information (ESI) available. See DOI: 10.1039/c3mb25485b Click here for additional data file.

Irene Papatheodorou, Janet M. Thornton, Matthias Ziehm, 2013, Molecular bioSystems.

MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans

Irene Papatheodorou, Janet M. Thornton, Jennifer M. A. Tullet, 2014, Aging.

Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases

Janet M. Thornton, Nicholas Furnham, Roman A. Laskowski, 2016, Journal of molecular biology.

Rebuilding flavodoxin from Cα coordinates: A test study

Janet M. Thornton, J. Thornton, L. Reid, 1989 .

Toward predicting protein topology: An approach to identifying β hairpins

Janet M. Thornton, Xavier de la Cruz, Adrian Shepherd, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Conformation of terminal regions in proteins

Janet M. Thornton, J. Thornton, Bancinyane L. Chakauya, 1982, Nature.

Understanding the molecular machinery of genetics through 3D structures

Janet M. Thornton, Roman A. Laskowski, J. Thornton, 2008, Nature Reviews Genetics.

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

Janet M. Thornton, Linda Partridge, Daniela Wieser, 2010, PLoS genetics.

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates

Neera Borkakoti, Janet M. Thornton, Jonathan D. Tyzack, 2018, Structure.

Using Answer Set Programming to Integrate RNA Expression with Signalling Pathway Information to Infer How Mutations Affect Ageing

Irene Papatheodorou, Janet M. Thornton, Linda Partridge, 2012, PloS one.

A combination of a functional motif model and a structural motif model for a database validation

Janet M. Thornton, Marialuisa Pellegrini-Calace, J. Thornton, 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.

Automatic inference of protein quaternary structure from crystals

Janet M. Thornton, J. Thornton, H. Ponstingl, 2003 .

Ribosomal Protein S6 Kinase 1 Signaling Regulates Mammalian Life Span

Janet M. Thornton, David Carling, Linda Partridge, 2009, Science.

Structural and sequence patterns in the loops of βαβ units

Janet M. Thornton, Michael J. E. Sternberg, M. Sternberg, 1987 .

Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

Janet M. Thornton, Abdellah Allali-Hassani, Alexander N. Plotnikov, 2007, PLoS Biology.

Topology-based protein structure comparison using a pattern discovery technique

David Gilbert, Janet M. Thornton, David R. Westhead, 2000 .

BLEEP—potential of mean force describing protein–ligand interactions: II. Calculation of binding energies and comparison with experimental data

Janet M. Thornton, Mark J. Forster, John B. O. Mitchell, 1999 .

Classifying a Protein Fold in the CATH Hierarchic Database

Janet M. Thornton, Christine A. Orengo, Acr Martin, 1998 .

Topological and stereochemical restrictions in β-sandwich protein structures

Janet M. Thornton, Derek N. Woolfson, J. Thornton, 1993 .

A global analysis of function and conservation of catalytic residues in enzymes

Neera Borkakoti, Janet M. Thornton, Gemma L. Holliday, 2019, The Journal of Biological Chemistry.

PDBe-KB: a community-driven resource for structural and functional annotations

Alfonso Valencia, Karel Berka, Jaroslav Koča, 2019, Nucleic Acids Res..

The implications of alternative splicing in the ENCODE protein complement

Hagen Blankenburg, Fidel Ramírez, Thomas Lengauer, 2007, Proceedings of the National Academy of Sciences.

On the conformation of proteins: an analysis of β-pleated sheets

Janet M. Thornton, Michael J. E. Sternberg, M. Sternberg, 1977 .

Protein-DNA Interactions

Helen M. Berman, Janet M. Thornton, Susan Jones, 1999 .

The interaction between phenylalanine rings in proteins

Janet M. Thornton, Juswinder Singh, J. Thornton, 1985 .

The future of bioinformatics

Janet M. Thornton, J. Thornton, 1998 .

Modelling by homology

Janet M. Thornton, Mark B. Swindells, M. Swindells, 1991 .

Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Chris Sander, Shoshana J. Wodak, Jean Richelle, 1998, Journal of molecular biology.

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies

Janet M. Thornton, Christine A. Orengo, Natalie L. Dawson, 2016, Journal of molecular biology.

Comparison of functional annotation schemes for genomes

Janet M. Thornton, Stuart C. G. Rison, J. Thornton, 2000, Functional & Integrative Genomics.

The shape of things to come?

Janet M. Thornton, J. Thornton, 1988, Nature.