Janet M. Thornton

According to our database1, Janet M. Thornton authored at least 75 papers between 1992 and 2019.

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Bibliography

2019
CATH: expanding the horizons of structure-based functional annotations for genome sequences.
Nucleic Acids Research, 2019

VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.
Bioinformatics, 2019

Finding enzyme cofactors in Protein Data Bank.
Bioinformatics, 2019

2018
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
Nucleic Acids Research, 2018

Transform-MinER: transforming molecules in enzyme reactions.
Bioinformatics, 2018

2016
Reaction Decoder Tool (RDT): extracting features from chemical reactions.
Bioinformatics, 2016

2015
Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.
PLoS Computational Biology, 2015

CATH: comprehensive structural and functional annotations for genome sequences.
Nucleic Acids Research, 2015

SurvCurv database and online survival analysis platform update.
Bioinformatics, 2015

2014
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
Nucleic Acids Research, 2014

The European Bioinformatics Institute's data resources 2014.
Nucleic Acids Research, 2014

PDBsum additions.
Nucleic Acids Research, 2014

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.
Bioinformatics, 2014

2013
Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset.
PLoS Computational Biology, 2013

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Nucleic Acids Research, 2013

The EBI enzyme portal.
Nucleic Acids Research, 2013

2012
Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies.
PLoS Computational Biology, 2012

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Nucleic Acids Research, 2012

Delivering ICT infrastructure for biomedical research.
Proceedings of the 2012 Joint Working IEEE/IFIP Conference on Software Architecture and European Conference on Software Architecture, 2012

2011
Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Nucleic Acids Research, 2011

2010
The European Bioinformatics Institute's data resources.
Nucleic Acids Research, 2010

The CoFactor database: organic cofactors in enzyme catalysis.
Bioinformatics, 2010

2009
PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure.
PLoS Computational Biology, 2009

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure.
PLoS Computational Biology, 2009

The CATH classification revisited - architectures reviewed and new ways to characterize structural divergence in superfamilies.
Nucleic Acids Research, 2009

Mapping Human Metabolic Pathways in the Small Molecule Chemical Space.
Journal of Chemical Information and Modeling, 2009

Small Molecule Subgraph Detector (SMSD) toolkit.
J. Cheminformatics, 2009

WSsas: a web service for the annotation of functional residues through structural homologues.
Bioinformatics, 2009

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Bioinformatics, 2009

Metal-MACiE: a database of metals involved in biological catalysis.
Bioinformatics, 2009

ELIXIR - A European Infrastructure for Biological Information: Challenges and Progress.
Proceedings of the Informatik 2009: Im Focus das Leben, 2009

2008
PROCOGNATE: a cognate ligand domain mapping for enzymes.
Nucleic Acids Research, 2008

The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Bioinformatics, 2008

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Proceedings of the ECCB'08 Proceedings, 2008

2007
Evolutionary Models for Formation of Network Motifs and Modularity in the Saccharomyces Transcription Factor Network.
PLoS Computational Biology, 2007

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data.
PLoS Computational Biology, 2007

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
Nucleic Acids Research, 2007

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
Nucleic Acids Research, 2007

Variation of geometrical and physicochemical properties in protein binding pockets and their ligands.
BMC Bioinformatics, 2007

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
Bioinformatics, 2007

2005
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
Nucleic Acids Research, 2005

ProFunc: a server for predicting protein function from 3D structure.
Nucleic Acids Research, 2005

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Nucleic Acids Research, 2005

The European Bioinformatics Institute's data resources: towards systems biology.
Nucleic Acids Research, 2005

Living longer by dieting: analysis of transcriptional response after caloric restriction.
BMC Bioinformatics, 2005

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.
Bioinformatics, 2005

MACiE: a database of enzyme reaction mechanisms.
Bioinformatics, 2005

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.
Bioinformatics, 2005

2004
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
Nucleic Acids Research, 2004

An examination of the conservation of surface patch polarity for proteins.
Bioinformatics, 2004

A practical and robust sequence search strategy for structural genomics target selection.
Bioinformatics, 2004

Microeconomic Principles Explain an Optimal Genome Size in Bacteria.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

ISMB/ECCB 2004 Organization.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

ISMB/ECCB 2004.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

SCOPEC: a database of protein catalytic domains.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Software Engineering Challenges in Bioinformatics.
Proceedings of the 26th International Conference on Software Engineering (ICSE 2004), 2004

2003
The CATH database: an extended protein family resource for structural and functional genomics.
Nucleic Acids Research, 2003

Gene3D: structural assignments for the biologist and bioinformaticist alike.
Nucleic Acids Research, 2003

Recognizing the fold of a protein structure.
Bioinformatics, 2003

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
Bioinformatics, 2003

The proteome and the metabolome.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002
A Computer System to Perform Structure Comparison using Representations of Protein Structure.
Computers & Chemistry, 2002

2001
A rapid classification protocol for the CATH Domain Database to support structural genomics.
Nucleic Acids Research, 2001

Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level.
Nucleic Acids Research, 2001

Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes.
Journal of Computational Chemistry, 2001

2000
Assigning genomic sequences to CATH.
Nucleic Acids Research, 2000

Une technique déclarative pour filtrer des motifs topologiques de protéines.
Proceedings of the Programmation en logique avec contraintes, 2000

1999
The CATH Database provides insights into protein structure/function relationships.
Nucleic Acids Research, 1999

BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential.
Journal of Computational Chemistry, 1999

BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data.
Journal of Computational Chemistry, 1999

Motif-based searching in TOPS protein topology databases.
Bioinformatics, 1999

1998
Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania.
Journal of Computer-Aided Molecular Design, 1998

[Invited Lecture] Protein Folds and Functions.
Proceedings of the German Conference on Bioinformatics, 1998

1993
Protein fold recognition.
Journal of Computer-Aided Molecular Design, 1993

1992
The rapid generation of mutation data matrices from protein sequences.
Computer Applications in the Biosciences, 1992


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