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List of works by Janet Thornton

1,000 structures and more from the MCSG.

scientific article

1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins

scientific article

A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus

scientific article

A bioinformatician's view of the metabolome

scientific article (publication date: 2006)

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

scientific article published on 22 April 2020

A computer system to perform structure comparison using TOPS representations of protein structure.

scientific article

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

scientific article published on 03 December 2019

A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli

scientific article

A method for localizing ligand binding pockets in protein structures

scientific article

A model recognition approach to the prediction of all-helical membrane protein structure and topology

scientific article

A mutation data matrix for transmembrane proteins

scientific article published on February 1994

A new approach to protein fold recognition

scientific article

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

scientific article

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

scientific article published on 26 October 2020

A novel degron-mediated degradation of the RTG pathway regulator, Mks1p, by SCFGrr1.

scientific article

A novel method for the modelling of peptide ligands to their receptors

scientific article published in February 1991

A nuclear magnetic resonance investigation of the conformation of nicotinamide mononucleotide in aqueous solution

scientific article

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

scientific article published on 16 June 2004

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

scientific article published in January 2001

A revised set of potentials for beta-turn formation in proteins

scientific article

A structural biology community assessment of AlphaFold 2 applications

A structural biology community assessment of AlphaFold2 applications

scientific article published in 2022

A structure-based anatomy of the E.coli metabolome

scientific article

A structured workflow for mapping human Sin3 histone deacetylase complex interactions using Halo-MudPIT AP-MS.

scientific article published on 29 March 2018

A study into the effects of protein binding on nucleotide conformation

scientific article published on March 1993

A study of structural determinants in the interleukin-1 fold

scientific article

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

scientific article

A topological model for hepatitis B surface antigen

scientific article published in January 1992

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR

scientific article (publication date: December 1996)

Abstracting knowledge from the protein data bank ⬇️

scientific article published on September 29, 2012

Accommodating sequence changes in beta-hairpins in proteins

scientific article published in January 1993

Activation of the SPS amino acid-sensing pathway in Saccharomyces cerevisiae correlates with the phosphorylation state of a sensor component, Ptr3.

scientific article

Adenosine Triphosphate (ATP) Is a Candidate Signaling Molecule in the Mitochondria-to-Nucleus Retrograde Response Pathway

scientific article published on 20 March 2013

Alpha plus beta folds revisited: some favoured motifs

scientific article

Amino acid architecture and the distribution of polar atoms on the surfaces of proteins

scientific article

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

scientific article

Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power

scientific article

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

scientific article (publication date: July 2001)

Amino and carboxy-terminal regions in globular proteins

scientific article published in June 1983

Amino/aromatic interactions

scientific article published in Nature

Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?

scientific article

An algorithm for automatically generating protein topology cartoons

scientific article

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

scientific article

An algorithm to compare secondary structure predictions

scientific article published in March 1984

An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure

scientific article

An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase ⬇️

scientific article published on February 25, 1978

An analysis of the three-dimensional structure of chicken triose phosphate isomerase

scientific article published on January 1, 1977

An atlas of protein topology cartoons available on the World-Wide Web.

scientific article

An examination of the conservation of surface patch polarity for proteins

scientific article

An extension of secondary structure prediction towards the prediction of tertiary structure

scientific article published on March 1991

An overview of the structures of protein-DNA complexes

scientific article

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data

scientific article

Analysis and prediction of carbohydrate binding sites

scientific article

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

scientific article

Analysis of catalytic residues in enzyme active sites

scientific article

Analysis of domain structural class using an automated class assignment protocol

scientific article

Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations

scientific article

Analysis of metabolic networks using a pathway distance metric through linear programming

scientific article

Analysis of protein main-chain solvation as a function of secondary structure

scientific article published on September 1991

Analysis of protein-protein interaction sites using surface patches

scientific article

Analysis, design and modification of loop regions in proteins

scientific article published on February 1988

Anna Tramontano 1957-2017.

scientific article published in May 2017

Annotations for all by all - the BioSapiens network

scientific article published on 10 February 2009

Antibody modelling. Tackling a loopy problem

scientific article published in February 1990

Antibody-antigen interactions: contact analysis and binding site topography.

scientific article

Assessment of comparative modeling in CASP2.

scientific article

Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.

scientific article

Assigning genomic sequences to CATH

scientific article published on January 2000

Atomic environments of arginine side chains in proteins

scientific article

Author Correction: Temporal changes in the gene expression heterogeneity during brain development and aging

scientific article published in 2023

Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels

scientific article

Beta-hairpin families in globular proteins

scientific article

Beta-turns and their distortions: a proposed new nomenclature

scientific article published in May 1990

Building and design

scientific article published in Nature

Buried waters and internal cavities in monomeric proteins

scientific article published on August 1994

CATH

database of protein domains structures

CATH--a hierarchic classification of protein domain structures

scientific article (publication date: 15 August 1997)

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

scientific article published on 01 January 2019

COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules.

scientific article

Calcium binding by troponin-C. A proton magnetic resonance study

scientific article published on October 1977

Catalysing new reactions during evolution: economy of residues and mechanism

scientific article

Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II

scientific article

Characterising Complex Enzyme Reaction Data

Characterising Complex Enzyme Reaction Data.

scientific article published on 3 February 2016

Characterization of Atypical Aeromonas salmonicida Different Methods ⬇️

scientific article published on March 1, 1998

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

scientific article published on 13 June 2011

ChemInform Abstract: Evolution of Enzymes and Pathways for the Biosynthesis of Cofactors

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

scientific article

Chromosome 5q candidate genes in coeliac disease: genetic variation at IL4, IL5, IL9, IL13, IL17B and NR3C1.

scientific article

Classifying a protein in the CATH database of domain structures

scientific article

Cognate Ligand Domain Mapping for Enzymes

scientific article

Comparison of conformational characteristics in structurally similar protein pairs

scientific article

Comparison of functional annotation schemes for genomes

scientific article

Comparison of the (2 x 2) reconstructions of GaAs{111} surfaces

scientific article

Comparison of the calcium- and magnesium-induced structural changes of troponin--C. A proton magnetic resonance study

scientific article published in July 1978

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

scientific article

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

scientific article published on 29 October 2015

Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.

scientific article

Computational biology for ageing

scientific article

Computer techniques for conformational studies of biological molecules

scientific article

Conformation of beta hairpins in protein structures: classification and diversity in homologous structures

scientific article published in January 1991

Conformation of terminal regions in proteins

scientific article published in July 1982

Conformation of β-hairpins in protein structures

article published in 1989

Conformational analysis of protein structures derived from NMR data

scientific article published on November 1993

Conformational change in substrate binding, catalysis and product release: an open and shut case?

scientific article published on June 2004

Conformational changes observed in enzyme crystal structures upon substrate binding

scientific article

Conformational diversity of ligands bound to proteins

scientific article published on 20 December 2005

Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3'-monophosphate

scientific article published on September 1975

Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate

scientific article

Conformational energy calculations for dinucleotide molecules: a study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+).

scientific article published on September 1977

Conservation helps to identify biologically relevant crystal contacts

scientific article

Construction, visualisation, and clustering of transcription networks from microarray expression data

scientific article

Contemporary approaches to protein structure classification

scientific article

Continuous and discontinuous protein antigenic determinants

scientific article published in August 1986

Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.

scientific article

Correcting for sequence biases in present/absent calls

scientific article published on January 2007

Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

scientific article

Correlation of observed fold frequency with the occurrence of local structural motifs

scientific article

Current challenges in genome annotation through structural biology and bioinformatics ⬇️

scientific article published on 09 August 2012

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 Caenorhabditis elegans

scientific article

DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.

scientific article

DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO

scientific article

Data Curation in Biology – Past, Present and Future

Data Curation in Biology – Past, Present and Future

Data-driven identification of ageing-related diseases from electronic health records

scientific article published on 3 February 2021

Delivering ICT infrastructure for biomedical research

Depicting topology and handedness in jellyroll structures

scientific article published in August 1992

Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases

scientific article published on June 1996

Design, synthesis and structure of a zinc finger with an artificial beta-turn

scientific article

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

scientific article

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

scientific article

Determinants of strand register in antiparallel beta-sheets of proteins

scientific article published on November 1998

Deviations from planarity of the peptide bond in peptides and proteins

scientific article

Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans

scientific article published on 7 March 2006

Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly

scientific article published in Scientific Reports

Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania.

scientific article

Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer's disease.

scientific article

Discriminating between homodimeric and monomeric proteins in the crystalline state

scientific article

Distributions of water around amino acid residues in proteins

scientific article published in August 1988

Disulphide bridges in globular proteins ⬇️

scientific article published on September 15, 1981

Diversity of protein-protein interactions

scientific article

Domain assignment for protein structures using a consensus approach: characterization and analysis

scientific article

Domain-ligand mapping for enzymes

scientific article published on March 2010

Donor activation and electronic screening at an antimony delta layer in silicon

scientific article

Drug repurposing for ageing research using model organisms

Drug repurposing for aging research using model organisms

scientific article published on 16 June 2017

EC-BLAST: a tool to automatically search and compare enzyme reactions

scientific article

ELIXIR: a distributed infrastructure for European biological data ⬇️

scientific article published on March 12, 2012

Editorial overview: Catalysis and regulation

scientific article published in December 2017

Effective function annotation through catalytic residue conservation

scientific article

Electrostatic interactions in proteins

scientific article published in January 1982

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity

scientific article

Elucidating human phosphatase-substrate networks

scientific article published on 14 May 2013

Emerging concepts in pseudoenzyme classification, evolution, and signaling

scientific article published on 13 August 2019

Endothelial-monocyte activating polypeptide II disrupts alveolar epithelial type II to type I cell transdifferentiation ⬇️

scientific article published on January 3, 2012

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]

scientific journal article

Estimation and correction of non-specific binding in a large-scale spike-in experiment

scientific article

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

Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice

scientific article

Evolution of binding sites for zinc and calcium ions playing structural roles

scientific article

Evolution of enzymes and pathways for the biosynthesis of cofactors

scientific article published on 12 September 2007

Evolution of function in protein superfamilies, from a structural perspective.

scientific article

Evolution of protein function, from a structural perspective

scientific article

Evolution of protein superfamilies and bacterial genome size

scientific article published in February 2004

Evolutionary conservation of regulated longevity assurance mechanisms

scientific article published on January 2007

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network

scientific article

Exploring Chemical Biosynthetic Design Space with Transform-MinER

scientific article published on 05 November 2019

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function

scientific article published on 01 January 2019

Exploring the biological and chemical complexity of the ligases

scientific article

Exploring the chemistry and evolution of the isomerases

scientific article published on 3 February 2016

Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies

scientific article

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

scientific article

Factors limiting the performance of prediction-based fold recognition methods

scientific article

Finding enzyme cofactors in Protein Data Bank

scientific article published on 01 September 2019

Fine-tuning autophagy maximises lifespan and is associated with changes in mitochondrial gene expression in Drosophila

scientific article published on 30 November 2020

From genome to function

scientific article

From protein structure to biochemical function?

scientific article

From protein structure to function.

scientific article

From structure to function: approaches and limitations

scientific article

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

scientific article

Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA.

scientific article

Gene Expression-Based Drug Repurposing to Target Ageing

article

Gene expression-based drug repurposing to target aging

article

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database

scientific article

Gene3D: structural assignments for the biologist and bioinformaticist alike

scientific article published on January 2003

Genome and proteome annotation: organization, interpretation and integration

scientific article

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling

scientific article

Genome-wide responses to mitochondrial dysfunction

scientific article

HERA--a program to draw schematic diagrams of protein secondary structures

scientific article

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

scientific article

Haplotype variation at the IBD5/SLC22A4 locus (5q31) in coeliac disease in the Irish population

scientific article published in August 2004

Haplotypes in the CTLA4 region are associated with coeliac disease in the Irish population

scientific article

Helix geometry in proteins

scientific article

Heme proteins--diversity in structural characteristics, function, and folding

scientific article published in August 2010

Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli

scientific article published on May 2002

Identification and classification of protein fold families

scientific article

Identification, classification, and analysis of beta-bulges in proteins

scientific article

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

scientific article

Identifying Potential Ageing-Modulating Drugs In Silico

scientific article published on 20 December 2018

Identifying pseudoenzymes using functional annotation. How loss of function correlates with mutations in the catalytic site

scientific article published on 16 November 2019

Iditis: protein structure database.

scientific article

In conversation with Janet Thornton

scientific article published on 01 October 2020

Inferring protein function from structure

scientific article

Influence of proline residues on protein conformation

scientific article published in March 1991

Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins

scientific article published on May 1990

Integrating Structure, Bioinformatics, and Enzymology to Discover Function: BioH, A NEW CARBOXYLESTERASE FROM ESCHERICHIA COLI

scientific article (publication date: 11 July 2003)

Integrating biological data through the genome

scientific article

Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein

scientific article

Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain

scientific article published on 5 January 2016

Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity

scientific article published in October 2017

Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures

scientific article

Introduction. Bioinformatics: from molecules to systems.

scientific article

Ion-pairs in proteins

scientific article published in August 1983

Just noticeable and objectionable group delays in digital hearing aids.

scientific article published on June 2000

Knowledge-based prediction of protein structures and the design of novel molecules

scientific article

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

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

scientific article (publication date: February 1995)

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

scientific article published on 13 November 2015

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

scientific article

Ligand selectivity and competition between enzymes in silico

scientific article

Lithium Promotes Longevity through GSK3/NRF2-Dependent Hormesis

scientific article published on 7 April 2016

Location of 'continuous' antigenic determinants in the protruding regions of proteins

scientific article published on February 1986

Long loops in proteins

scientific article published on November 1995

Longevity GWAS Using the Drosophila Genetic Reference Panel

scientific article

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

scientific article (publication date: 3 January 2007)

MACiE: a database of enzyme reaction mechanisms

scientific article (publication date: December 2005)

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

scientific article published on February 2014

Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium

scientific article published on July 1996

Main-chain bond lengths and bond angles in protein structures

scientific article (publication date: 20 June 1993)

Mapping human metabolic pathways in the small molecule chemical space

scientific article published in October 2009

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

scientific article published on 2 November 2017

Metabolic innovations towards the human lineage

scientific article published on 9 September 2008

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

scientific article published on 5 July 2008

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

scholarly article by Claudia Andreini et al published 15 April 2009 in Bioinformatics

Microeconomic principles explain an optimal genome size in bacteria

scientific article published in January 2005

Minimum information about a bioactive entity (MIABE).

scientific article

Missing in action: enzyme functional annotations in biological databases

scientific article published on August 2009

Mitochondria-to-nuclear signaling is regulated by the subcellular localization of the transcription factors Rtg1p and Rtg3p

scientific article

Modeling studies of the change in conformation required for cleavage of limited proteolytic sites

scientific article published on May 1994

Modelling antibody combining sites: a review.

scientific article published on January 1991

Modelling protein unfolding: hen egg-white lysozyme

scientific article

Molecular Sociology

Molecular Sociology

Molecular basis for DPY-30 association to COMPASS-like and NURF complexes

scientific article

Molecular basis of inherited diseases: a structural perspective

scientific article

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases

scientific article

Molecular modelling and epitope prediction of gp29 from lymphatic filariae

scientific article published in March 1993

Molecular recognition by proteins: protein-ligand interactions from a structural perspective

scientific article

Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors

scientific article

Morphological aspects of oligomeric protein structures

scientific article

Motif-based searching in TOPS protein topology databases

scientific article

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

scientific article

NMR and crystallography--complementary approaches to structure determination

scientific article published on May 1994

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions

scientific article published on December 1997

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

scientific article

New open drug activity data at EBI

New tools and resources for analysing protein structures and their interactions

scientific article

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

scientific article

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

scholarly article by John B.O. Mitchell published in November 1997

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

scientific article published in February 1977

On the conformation of proteins: hydrophobic ordering of strands in beta-pleated sheets

scientific article published in September 1977

On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit

scientific article published in August 1976

On the conformation of proteins: the handedness of the connection between parallel beta-strands

scientific article published in February 1977

On the conformation of proteins: towards the prediction of strand arrangements in beta-pleated sheets

scientific article published in June 1977

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins

scientific article

On the molecular discrimination between adenine and guanine by proteins

scientific article published on November 2001

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions

scientific article (publication date: 30 August 2002)

PDBsum additions

scientific article

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

scientific article

PDBsum: Structural summaries of PDB entries

scientific article published on 5 September 2017

PDBsum: a Web-based database of summaries and analyses of all PDB structures

scientific article

PQS: a protein quaternary structure file server

scientific article

PROCHECK: a program to check the stereochemical quality of protein structures

scientific article

PROCOGNATE: a cognate ligand domain mapping for enzymes

scientific article published on 24 August 2007

PROMOTIF--a program to identify and analyze structural motifs in proteins

scientific article

PROTEIN FAMILIES AND THEIR EVOLUTION—A STRUCTURAL PERSPECTIVE

scientific article

PROTEIN MOTIFS AND DATA-BASE SEARCHING

article

PROTEIN NUCLEIC ACID INTERACTIONS GRANT # DE-FG02-96ER62166 FINAL REPORT

Pathway evolution, structurally speaking

scientific article

Peptide-protein interactions: an overview.

scientific article published on August 1993

Pharamacological agents for managing symptoms in people with cystic fibrosis-related arthritis

scientific article

Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins

scientific article published in April 1991

Plasticity of enzyme active sites

scientific article

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

scientific article published on 17 September 2009

PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure

scientific article

Potential energy functions for threading

scientific article

Predicting protein function from sequence and structural data.

scientific article

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure

scientific article

Prediction of protein function from structure: insights from methods for the detection of local structural similarities

scientific article

Prediction of protein structure from amino acid sequence

scientific article published on 01 January 1978

Prediction of protein structure from amino acid sequence

scientific article published in Nature

Prediction of protein-protein interaction sites using patch analysis

scientific article

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

scientific article

Prediction of super-secondary structure in proteins

scientific article published in February 1983

Prediction of the location and type of beta-turns in proteins using neural networks.

scientific article published on May 1999

Prepublication data sharing

scientific article

Principles of protein-protein interactions

scientific article (publication date: 9 January 1996)

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

scientific article

Progress of structural genomics initiatives: an analysis of solved target structures.

scientific article

Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease

article

Protein Quaternary Structure: Subunit-Subunit Interactions

Protein Structure Classification

Protein clefts in molecular recognition and function

scientific article published on December 1996

Protein domain interfaces: characterization and comparison with oligomeric protein interfaces

scientific article

Protein fold recognition

scientific article

Protein fold recognition by sequence threading: tools and assessment techniques

scientific article published on January 1996

Protein folds and functions

scientific article

Protein folds, functions and evolution

scientific article

Protein folds: towards understanding folding from inspection of native structures

scientific article

Protein function annotation by homology-based inference

scientific article (publication date: 2 February 2009)

Protein function prediction using local 3D templates

scientific article

Protein motifs and data-base searching.

scientific article

Protein promiscuity and its implications for biotechnology

scientific article published on February 2009

Protein recognition of adenylate: an example of a fuzzy recognition template

scientific article

Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states?

scientific article

Protein structural topology: Automated analysis and diagrammatic representation.

scientific article published on April 1999

Protein structure Prediction

article from 1998

Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.

scientific article published on 20 June 2017

Protein structure. Prediction of progress at last

scientific article published in November 1991

Protein structure. The shape of things to come?

scientific article published in September 1988

Protein superfamilies and domain superfolds

scientific article (publication date: 15 December 1994)

Protein superfamily evolution and the last universal common ancestor (LUCA).

scientific article

Protein-DNA interactions: A structural analysis

scientific article published on April 1999

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity

scientific article

Protein-DNA interactions: the story so far and a new method for prediction

scientific article

Protein-RNA interactions: a structural analysis

scientific article

Protein-protein interactions: a review of protein dimer structures

scientific article published on January 1995

Protein-protein interfaces: analysis of amino acid conservation in homodimers

scientific article

Protein-protein recognition via side-chain interactions

scientific article

Proteins: interaction at a distance

scientific article published on 30 October 2015

Proton magnetic resonance study of troponin-C.

scientific article published on January 1976

Quantifying the similarities within fold space

scientific article

Quantitative determination of the conformation of ATP in aqueous solution using the lanthanide cations as nuclear-magnetic-resonance probes

scientific article

RTG-dependent mitochondria-to-nucleus signaling is regulated by MKS1 and is linked to formation of yeast prion [URE3]

scientific article

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

scientific article

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

scientific article (publication date: July 2016)

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

scientific article

Rebuilding flavodoxin from C alpha coordinates: a test study

scientific article published in January 1989

Recognition of super-secondary structure in proteins

Recognizing the fold of a protein structure.

scientific article

Recurrence of a binding motif?

scientific article published in March 1993

Recurring structural motifs in proteins with different functions

scientific article published in March 1993

Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk

scientific article

Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins

scientific article

Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins

scientific article

Retrograde response to mitochondrial dysfunction is separable from TOR1/2 regulation of retrograde gene expression

scientific article

Retrograde signaling is regulated by the dynamic interaction between Rtg2p and Mks1p

scientific article

Ribosomal protein S6 kinase 1 signaling regulates mammalian life span

scientific article (publication date: 2 October 2009)

SCOPEC: a database of protein catalytic domains.

scientific article

SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups

scientific article published in February 1990

SPINE bioinformatics and data-management aspects of high-throughput structural biology

scientific article

Satisfying hydrogen bonding potential in proteins

scientific article (publication date: 20 May 1994)

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

scientific article published on 14 August 2019

Searching for functional sites in protein structures.

scientific article

Sequence and structural differences between enzyme and nonenzyme homologs

scientific article published in October 2002

Sequences and topology

scientific article

Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis

scientific article

Shape variation in protein binding pockets and their ligands

scientific article

Shared structural motif in proteins

scientific article published in Nature

Shouldn't enantiomeric purity be included in the 'minimum information about a bioactive entity? Response from the MIABE group

Small Molecule Subgraph Detector (SMSD) toolkit

scientific article

Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage

scientific article

Small subunit rRNA gene sequences of Aeromonas salmonicida subsp. smithia and Haemophilus piscium reveal pronounced similarities with A. salmonicida subsp. salmonicida

scientific article

Small-molecule metabolism: an enzyme mosaic

scientific article

Solution structure of a biologically active cyclic LDV peptide analogue containing a type II' beta-turn mimetic.

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Solvent-induced distortions and the curvature of alpha-helices

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Stereochemical quality of protein structure coordinates

scientific article (publication date: April 1992)

Strain relaxation during the initial stages of growth in Ge/Si(001).

scientific article published in February 1991

Structural Patterns in Globular Proteins

Structural analysis of metal sites in proteins: non-heme iron sites as a case study

scientific article published on 2 March 2009

Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate

scientific article published on 29 April 2020

Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders

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Structural and chemical profiling of the human cytosolic sulfotransferases

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Structural and sequence patterns in the loops of beta alpha beta units

scientific article published in June 1987

Structural bioinformatics: from protein structure to function

Structural characterisation and functional significance of transient protein-protein interactions

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Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies

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Structural genomics takes off.

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Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity

scientific article published on October 1995

Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).

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Structural survey

scientific article published in Nature

Structure prediction and modelling.

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Structures of N-termini of helices in proteins

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Substrate recognition by proteinases

scientific article published in January 1992

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

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SurvCurv database and online survival analysis platform update

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TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites ⬇️

scientific article published on November 1997

THE RAMACHANDRAN PLOT AND PROTEIN STRUCTURE VALIDATION

TORC2 Signaling Is Antagonized by Protein Phosphatase 2A and the Far Complex in Saccharomyces cerevisiae ⬇️

scientific article published on January 31, 2012

Target selection and determination of function in structural genomics

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Temporal changes in the gene expression heterogeneity during brain development and aging

scientific article published on 05 March 2020

The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.

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The (non)malignancy of cancerous amino acidic substitutions

scientific article published in February 2010

The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions

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The CATH Database provides insights into protein structure/function relationships.

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The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues

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

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

scientific article published on 7 November 2008

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

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The CATH domain structure database.

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

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The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space

scientific article published on August 2009

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

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The CCPN project: an interim report on a data model for the NMR community

scientific article

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

scientific article

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

scientific article (publication date: 2004)

The Classification and Evolution of Enzyme Function

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The CoFactor database: organic cofactors in enzyme catalysis

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The EBI enzyme portal

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The European Bioinformatics Institute's data resources

scientific article (publication date: 2010)

The European Bioinformatics Institute's data resources 2014

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

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The European dimension for the mouse genome mutagenesis program

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The Evolution of Enzyme Mechanisms and Functional Diversity

The Greek key motif: extraction, classification and analysis

scientific article

The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution

scientific article published on January 2001

The NAD Binding Domain and the Short-Chain Dehydrogenase/Reductase (SDR) Superfamily

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

scientific article

The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative

scientific article

The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains

scientific article

The chemistry of protein catalysis.

scientific article

The complement of enzymatic sets in different species

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The distribution of charged groups in proteins

scientific article published in September 1986

The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli

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The evolution of enzyme function in the isomerases

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The fine details of evolution

scientific article published in August 2009

The geometries of interacting arginine-carboxyls in proteins

scientific article published in November 1987

The geometry of interactions between catalytic residues and their substrates

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The history of the CATH structural classification of protein domains

scientific article (publication date: December 2015)

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The little elongation complex regulates small nuclear RNA transcription

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The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides

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The new science of ageing

scientific article published on September 2015

The new science of ageing

scientific article published on January 2011

The rapid generation of mutation data matrices from protein sequences

scientific article (publication date: June 1992)

The structural basis of allosteric regulation in proteins

scientific article published on 18 March 2009

The structures and physicochemical properties of organic cofactors in biocatalysis

scientific article published on 17 September 2010

The widespread increase in inter-individual variability of gene expression in the human brain with age

article

Three-dimensional structure analysis of PROSITE patterns

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To what extent do structural changes in catalytic metal sites affect enzyme function?

scientific article published on 8 November 2017

Topological and stereochemical restrictions in beta-sandwich protein structures

scientific article published on July 1993

Toward predicting protein topology: an approach to identifying beta hairpins.

scientific article

Toward the detection and validation of repeats in protein structure.

scientific article

Towards an understanding of the arginine-aspartate interaction.

scientific article published in July 1992

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

scientific article published on April 1996

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster ⬇️

scientific article published on April 26, 2013

Transform-MinER: Transforming Molecules in Enzyme Reactions

scientific article published on 01 October 2018

Understanding enzyme function evolution from a computational perspective

scientific article published on 7 September 2017

Understanding nature's catalytic toolkit

scientific article

Understanding the functional roles of amino acid residues in enzyme catalysis.

scientific article published on 15 May 2009

Understanding the molecular machinery of genetics through 3D structures

scientific article published on February 2008

Unlocking the potential of survival data for model organisms through a new database and online analysis platform:SurvCurv ⬇️

scientific article (publication date: October 2013)

Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families

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Using a neural network and spatial clustering to predict the location of active sites in enzymes

scientific article

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing

scientific article

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

scientific article

Using structural motif templates to identify proteins with DNA binding function

scientific article published in June 2003

Using the CATH domain database to assign structures and functions to the genome sequences

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Using the drug-protein interactome to identify anti-ageing compounds for humans

Using the drug-protein interactome to identify anti-ageing compounds for humans

scientific article published on 09 January 2019

Validation of protein models derived from experiment

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

scientific article published on 01 November 2019

VarSite: Disease variants and protein structure

scientific article published on 27 October 2019

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

scientific article published on 20 November 2007

WDR76 Co-Localizes with Heterochromatin Related Proteins and Rapidly Responds to DNA Damage

scientific article (publication date: 2016)

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

scientific article published on 27 February 2009

Wavelet transforms for the characterization and detection of repeating motifs

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What you need to know to make the most of big data in biology

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Women in Science

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X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins

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cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches

scientific article published on 19 September 2017

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