Exploring the biological and chemical complexity of the ligases.
EC-BLAST: a tool to automatically search and compare enzyme reactions.
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.
Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.
Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.
Elucidating human phosphatase-substrate networks.
Abstracting knowledge from the protein data bank.
The EBI enzyme portal.
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Current challenges in genome annotation through structural biology and bioinformatics.
ELIXIR: a distributed infrastructure for European biological data.
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Women in science.
Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II.
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.
The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.
Minimum information about a bioactive entity (MIABE).
The new science of ageing.
Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Computational biology for ageing.
Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling.
1,000 structures and more from the MCSG.
The structures and physicochemical properties of organic cofactors in biocatalysis.
The CoFactor database: organic cofactors in enzyme catalysis.
Heme proteins--diversity in structural characteristics, function, and folding.
DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.
On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.
Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk.
Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.
The (non)malignancy of cancerous amino acidic substitutions.
The European Bioinformatics Institute's data resources.
Domain-ligand mapping for enzymes.
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Enhanced DNA binding capacity on up-regulated epidermal wild-type p53 in vitiligo by H2O2-mediated oxidation: a possible repair mechanism for DNA damage.
Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Mapping human metabolic pathways in the small molecule chemical space.
Prepublication data sharing.
The fine details of evolution.
The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.
Missing in action: enzyme functional annotations in biological databases.
Metal-MACiE: a database of metals involved in biological catalysis.
Understanding the functional roles of amino acid residues in enzyme catalysis.
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
The structural basis of allosteric regulation in proteins.
WSsas: a web service for the annotation of functional residues through structural homologues.
Structural analysis of metal sites in proteins: non-heme iron sites as a case study.
The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.
Protein promiscuity and its implications for biotechnology.
Genome and proteome annotation: organization, interpretation and integration.
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
Small Molecule Subgraph Detector (SMSD) toolkit.
Protein function annotation by homology-based inference.
Annotations for all by all - the BioSapiens network.
New open drug activity data at EBI
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Metal ions in biological catalysis: from enzyme databases to general principles.
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Evolution of binding sites for zinc and calcium ions playing structural roles.
Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice.
Understanding the molecular machinery of genetics through 3D structures.
PROCOGNATE: a cognate ligand domain mapping for enzymes.
Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Activation of the SPS amino acid-sensing pathway in Saccharomyces cerevisiae correlates with the phosphorylation state of a sensor component, Ptr3.
Metabolic innovations towards the human lineage.
The chemistry of protein catalysis.
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
Evolution of enzymes and pathways for the biosynthesis of cofactors.
Construction, visualisation, and clustering of transcription networks from microarray expression data.
The geometry of interactions between catalytic residues and their substrates.
Structural and chemical profiling of the human cytosolic sulfotransferases.
Towards fully automated structure-based function prediction in structural genomics: a case study.
Shape variation in protein binding pockets and their ligands.
The implications of alternative splicing in the ENCODE protein complement.
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
Evolutionary conservation of regulated longevity assurance mechanisms.
Estimation and correction of non-specific binding in a large-scale spike-in experiment.
Correcting for sequence biases in present/absent calls.
Erratum to "Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans" [Mech. Ageing Dev. 127 (5) (2006) 458-472].
Cognate ligand domain mapping for enzymes.
Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.
SPINE bioinformatics and data-management aspects of high-throughput structural biology.
Protein superfamily evolution and the last universal common ancestor (LUCA).
Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans.
An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.
A bioinformatician's view of the metabolome.
Integrating biological data through the genome.
Introduction. Bioinformatics: from molecules to systems.
Conformational diversity of ligands bound to proteins.
A method for localizing ligand binding pockets in protein structures.
Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins.
Retrograde response to mitochondrial dysfunction is separable from TOR1/2 regulation of retrograde gene expression.
MACiE: a database of enzyme reaction mechanisms.
Understanding nature's catalytic toolkit.
A novel degron-mediated degradation of the RTG pathway regulator, Mks1p, by SCFGrr1.
Morphological aspects of oligomeric protein structures.
Protein function prediction using local 3D templates.
Effective function annotation through catalytic residue conservation.
ProFunc: a server for predicting protein function from 3D structure.
The complement of enzymatic sets in different species.
Prediction of protein function from structure: insights from methods for the detection of local structural similarities.
Predicting protein function from sequence and structural data.
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.
Progress of structural genomics initiatives: an analysis of solved target structures.
Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families.
A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.
Conformational changes observed in enzyme crystal structures upon substrate binding.
The European Bioinformatics Institute's data resources: towards systems biology.
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Microeconomic principles explain an optimal genome size in bacteria.
Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins.
Protein families and their evolution-a structural perspective.
Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.
Toward the detection and validation of repeats in protein structure.
A practical and robust sequence search strategy for structural genomics target selection.
SCOPEC: a database of protein catalytic domains.
Ligand selectivity and competition between enzymes in silico.
Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.
Conformational change in substrate binding, catalysis and product release: an open and shut case?
Searching for functional sites in protein structures.
Evolution of protein superfamilies and bacterial genome size.
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
A structure-based anatomy of the E.coli metabolome.
Recognizing the fold of a protein structure.
Molecular basis of inherited diseases: a structural perspective.
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
Catalysing new reactions during evolution: economy of residues and mechanism.
A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.
Using a neural network and spatial clustering to predict the location of active sites in enzymes.
Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.
Diversity of protein-protein interactions.
Analysis of metabolic networks using a pathway distance metric through linear programming.
Using structural motif templates to identify proteins with DNA binding function.
Sequences and topology.
A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks.
Structural characterisation and functional significance of transient protein-protein interactions.
Gene3D: structural assignments for the biologist and bioinformaticist alike.
Target selection and determination of function in structural genomics.
Protein-DNA interactions: the story so far and a new method for prediction.
Inferring protein function from structure.
From protein structure to biochemical function?
Quantifying the similarities within fold space.
Analysis of catalytic residues in enzyme active sites.
Sequence and structural differences between enzyme and nonenzyme homologs.
Toward predicting protein topology: an approach to identifying beta hairpins.
Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.
Plasticity of enzyme active sites.
One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
The CCPN project: an interim report on a data model for the NMR community.
Pathway evolution, structurally speaking.
Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.
RTG-dependent mitochondria-to-nucleus signaling is regulated by MKS1 and is linked to formation of yeast prion [URE3].
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.
Wavelet transforms for the characterization and detection of repeating motifs.
Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein.
The CATH protein family database: a resource for structural and functional annotation of genomes.
Prediction of protein structure from amino acid sequence.
Prediction of protein structure from amino acid sequence.
On the conformation of proteins: hydrophobic ordering of strands in beta-pleated sheets.
On the conformation of proteins: towards the prediction of strand arrangements in beta-pleated sheets.
On the conformation of proteins: the handedness of the connection between parallel beta-strands.
On the conformation of proteins: an analysis of beta-pleated sheets.
An analysis of the three-dimensional structure of chicken triose phosphate isomerase.
On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit.
Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate.
Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3'-monophosphate.
Topology-based protein structure comparison using a pattern discovery technique (Extended Abstract)
The Ramachandran plot and protein structure validation
Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease
Protein Data Resources
A Constraint-Based System for Protein Motif-Searching, Pattern Discovery and Structure Comparison
A Constraint--Based System for Protein Motif--Searching, Pattern Discovery and Structure Comparison
A Constraint--Based System for Protein Motif--Searching, Pattern Discovery and Structure Comparison
A Constraint--Based System for Protein Motif--Searching, Pattern Discovery and Structure Comparison
A computer system to perform structure comparison using TOPS representations of protein structure
HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.
Amino acid architecture and the distribution of polar atoms on the surfaces of proteins.
Chromosome 5q candidate genes in coeliac disease: genetic variation at IL4, IL5, IL9, IL13, IL17B and NR3C1.
An examination of the conservation of surface patch polarity for proteins.
Haplotype variation at the IBD5/SLC22A4 locus (5q31) in coeliac disease in the Irish population.
The CATH domain structure database.
Small-molecule metabolism: an enzyme mosaic.
The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.
On the molecular discrimination between adenine and guanine by proteins.
Conservation helps to identify biologically relevant crystal contacts.
The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli.
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
From genome to function.
Evolution of function in protein superfamilies, from a structural perspective.
Protein-RNA interactions: a structural analysis.
The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution.
Protein-protein interfaces: analysis of amino acid conservation in homodimers.
A rapid classification protocol for the CATH Domain Database to support structural genomics.
From structure to function: approaches and limitations.
Discriminating between homodimeric and monomeric proteins in the crystalline state.
Comparison of functional annotation schemes for genomes.
The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.
Using the CATH domain database to assign structures and functions to the genome sequences.
Protein domain interfaces: characterization and comparison with oligomeric protein interfaces.
Analysis and prediction of carbohydrate binding sites.
Assigning genomic sequences to CATH.
An overview of the structures of protein-DNA complexes.
Protein folds, functions and evolution.
Evolution of protein function, from a structural perspective.
Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
Polymerase chain reaction (PCR)-based typing analysis of atypical isolates of the fish pathogen Aeromonas salmonicida.
From protein structure to function.
Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states?
Prediction of the location and type of beta-turns in proteins using neural networks.
DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.
Protein-DNA interactions: A structural analysis.
Protein structural topology: Automated analysis and diagrammatic representation.
Factors limiting the performance of prediction-based fold recognition methods.
Correlation of observed fold frequency with the occurrence of local structural motifs.
Three-dimensional structure analysis of PROSITE patterns.
The CATH Database provides insights into protein structure/function relationships.
Small subunit rRNA gene sequences of Aeromonas salmonicida subsp. smithia and Haemophilus piscium reveal pronounced similarities with A. salmonicida subsp. salmonicida.
New tools and resources for analysing protein structures and their interactions.
Determinants of strand register in antiparallel beta-sheets of proteins.
Contemporary approaches to protein structure classification.
Classifying a protein in the CATH database of domain structures.
Validation of protein models derived from experiment.
Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
Evolution of the androgen receptor: structure-function implications.
PQS: a protein quaternary structure file server.
Protein structure prediction.
1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins.
Protein folds and functions.
Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania.
Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.
Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage.
Characterization of atypical Aeromonas salmonicida by different methods.
Domain assignment for protein structures using a consensus approach: characterization and analysis.
Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).
An atlas of protein topology cartoons available on the World-Wide Web.
PDBsum: a Web-based database of summaries and analyses of all PDB structures.
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
Non-randomness in side-chain packing: the distribution of interplanar angles.
Prediction of protein-protein interaction sites using patch analysis.
Analysis of protein-protein interaction sites using surface patches.
Modelling protein unfolding: hen egg-white lysozyme.
CATH--a hierarchic classification of protein domain structures.
Structures of N-termini of helices in proteins.
Assessment of comparative modeling in CASP2.
Protein clefts in molecular recognition and function.
Multiple solution conformations of the integrin-binding cyclic pentapeptide cyclo(-Ser-D-Leu-Asp-Val-Pro-). Analysis of the (phi, psi) space available to cyclic pentapeptides.
Deviations from planarity of the peptide bond in peptides and proteins.
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies.
Protein recognition of adenylate: an example of a fuzzy recognition template.
Antibody-antigen interactions: contact analysis and binding site topography.
Analysis of domain structural class using an automated class assignment protocol.
Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium.
Solution structure of a biologically active cyclic LDV peptide analogue containing a type II' beta-turn mimetic.
Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases.
X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins.
Towards meeting the Paracelsus Challenge: The design, synthesis, and characterization of paracelsin-43, an alpha-helical protein with over 50% sequence identity to an all-beta protein.
Potential energy functions for threading.
PROMOTIF--a program to identify and analyze structural motifs in proteins.
Molecular recognition by proteins: protein-ligand interactions from a structural perspective.
Protein fold recognition by sequence threading: tools and assessment techniques.
Principles of protein-protein interactions.
Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.
Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA.
Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
Long loops in proteins.
Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity.
Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures.
Protein folds: towards understanding folding from inspection of native structures.
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
Protein-protein interactions: a review of protein dimer structures.
Protein superfamilies and domain superfolds.
A revised set of potentials for beta-turn formation in proteins.
Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?
Satisfying hydrogen bonding potential in proteins.
NMR and crystallography--complementary approaches to structure determination.
Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
A model recognition approach to the prediction of all-helical membrane protein structure and topology.
The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions.
An algorithm for automatically generating protein topology cartoons.
Conformational analysis of protein structures derived from NMR data.
Comparison of conformational characteristics in structurally similar protein pairs.
Identification, classification, and analysis of beta-bulges in proteins.
Alpha plus beta folds revisited: some favoured motifs.
A study of structural determinants in the interleukin-1 fold.
Peptide-protein interactions: an overview.
Topological and stereochemical restrictions in beta-sandwich protein structures.
Identification and classification of protein fold families.
Main-chain bond lengths and bond angles in protein structures.
The Greek key motif: extraction, classification and analysis.
PROCHECK: a program to check the stereochemical quality of protein structures.
Atomic environments of arginine side chains in proteins.
Recurring structural motifs in proteins with different functions.
Recurrence of a binding motif?
Molecular modelling and epitope prediction of gp29 from lymphatic filariae.
A study into the effects of protein binding on nucleotide conformation.
Accommodating sequence changes in beta-hairpins in proteins.
Towards an understanding of the arginine-aspartate interaction.
A new approach to protein fold recognition.
The rapid generation of mutation data matrices from protein sequences.
Stereochemical quality of protein structure coordinates.
Substrate recognition by proteinases.
A topological model for hepatitis B surface antigen.
Protein structure. Prediction of progress at last.
Analysis of protein main-chain solvation as a function of secondary structure.
Structure prediction and modelling.
Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors.
Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins.
Influence of proline residues on protein conformation.
A novel method for the modelling of peptide ligands to their receptors.
Conformation of beta hairpins in protein structures: classification and diversity in homologous structures.
Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins.
Beta-turns and their distortions: a proposed new nomenclature.
SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups.
HERA--a program to draw schematic diagrams of protein secondary structures.
Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power.
Protein motifs and data-base searching.
Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering.
Rebuilding flavodoxin from C alpha coordinates: a test study.
Protein-protein recognition via side-chain interactions.
Protein structure. The shape of things to come?
Analysis and prediction of the different types of beta-turn in proteins.
Distributions of water around amino acid residues in proteins.
Helix geometry in proteins.
Analysis, design and modification of loop regions in proteins.
The geometries of interacting arginine-carboxyls in proteins.
Structural and sequence patterns in the loops of beta alpha beta units.
Knowledge-based prediction of protein structures and the design of novel molecules.
The distribution of charged groups in proteins.
Location of 'continuous' antigenic determinants in the protruding regions of proteins.
Continuous and discontinuous protein antigenic determinants.
Beta-hairpin families in globular proteins.
Recognition of super-secondary structure in proteins.
Ion-pairs in proteins.
Amino and carboxy-terminal regions in globular proteins.
Prediction of super-secondary structure in proteins.
Conformation of terminal regions in proteins.
Electrostatic interactions in proteins.
Disulphide bridges in globular proteins.
An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase.
Calcium binding by troponin-C. A proton magnetic resonance study.
Conformational energy calculations for dinucleotide molecules: a study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+).
Quantitative determination of the conformation of ATP in aqueous solution using the lanthanide cations as nuclear-magnetic-resonance probes.