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