Search filters

List of works by Christine Orengo

1,000 structures and more from the MCSG.

scientific article

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

scientific article published in 2022

A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations

scientific article published in Scientific Reports

A fast and automated solution for accurately resolving protein domain architectures.

scientific article

A holistic approach to protein structure alignment

scientific article

A large-scale evaluation of computational protein function prediction

scientific article

A local alignment method for protein structure motifs

scientific article

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

scientific article published on 16 June 2004

A protein structure comparison methodology

article

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

scientific article published in January 2001

A rapid method of protein structure alignment

scientific article

A structural perspective on genome evolution

scientific article

Alpha plus beta folds revisited: some favoured motifs

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D.

scientific article

An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences

scientific article published on 28 July 2017

Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction

scientific article

Analysis of domain structural class using an automated class assignment protocol

scientific article

Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.

scientific article published on 18 October 2017

Assessing strategies for improved superfamily recognition

scientific article published on 3 June 2005

Assessment of protein domain fusions in human protein interaction networks prediction: application to the human kinetochore model

scientific article published on 17 September 2010

Assigning genomic sequences to CATH

scientific article published on January 2000

Association of serum cholesterol and triglyceride levels with agitation and cognitive function in a geropsychiatry unit

scientific article

Behavioral disturbances in geropsychiatric inpatients across dementia types

scientific article

CATH

database of protein domains structures

CATH FunFHMMer web server: protein functional annotations using functional family assignments

scientific article published on 11 May 2015

CATH--a hierarchic classification of protein domain structures

scientific article (publication date: 15 August 1997)

CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences

scientific article

CATH: an expanded resource to predict protein function through structure and sequence

scientific article

CATH: comprehensive structural and functional annotations for genome sequences.

scientific article

CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

scientific article

CODA: accurate detection of functional associations between proteins in eukaryotic genomes using domain fusion

scientific article

CORA--topological fingerprints for protein structural families

scientific article published on April 1999

Cancer-associated mutations are preferentially distributed in protein kinase functional sites

scientific article published in December 2009

Chainsaw: protein domain segmentation with fully convolutional neural networks

Chapter 1. Target selection in structural genomics projects to increase knowledge of protein structure and function space

scientific article

Characterization of pathogenic germline mutations in human protein kinases

scientific article

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia

scientific article published on 27 June 2022

Choosing the Best Enzyme Complex Structure Made Easy

scientific article published in April 2018

Classifying a protein in the CATH database of domain structures

scientific article

Clinical and ethical implications of impaired executive control functions for patient autonomy

scientific article

Co-Expression Network Models Suggest that Stress Increases Tolerance to Mutations

scientific article

Combining sensitive database searches with multiple intermediates to detect distant homologues

scientific article

Comparative evolutionary analysis of protein complexes in E. coli and yeast

scientific article published on February 2010

Comparison of conformational characteristics in structurally similar protein pairs

scientific article

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space

scientific article

Consensus clustering and functional interpretation of gene-expression data

scientific article

Contemporary approaches to protein structure classification

scientific article

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

scientific article

Crystal structures of the human Dysferlin inner DysF domain

scientific article

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

scientific article

Delirium in geropsychiatric patients: patient characteristics and treatment outcomes

scientific article

Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification

scientific article

Domain Family Analyses to Understand Protein Function Evolution

scientific article published on 12 July 2010

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

scientific article

Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer

scientific article published on 25 December 2008

ENFIN--A European network for integrative systems biology

scientific article

Editorial overview: Catalysis and regulation

scientific article published in December 2017

Editorial overview: Sequences and topology: sequences, structures, genomes and populations

scientific article

Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips

scientific article

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 history of the TBP-domain superfamily

scientific article

Exploiting protein structure data to explore the evolution of protein function and biological complexity.

scientific article

Exploiting structural classifications for function prediction: towards a domain grammar for protein function.

scientific article

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

scientific article published on 01 January 2019

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

scientific article

Exploring the structure and function paradigm.

scientific article

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

scientific article

EyeSite: a semi-automated database of protein families in the eye.

scientific article

FFPred: an integrated feature-based function prediction server for vertebrate proteomes

scientific article

FLORA: a novel method to predict protein function from structure in diverse superfamilies

scientific article

FUN-L: gene prioritization for RNAi screens

scientific article published on 08 February 2015

Fast structure alignment for protein databank searching

scientific article published on October 1, 1992

Finding the "dark matter" in human and yeast protein network prediction and modelling

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

Function Diversity Within Folds and Superfamilies

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

scientific article

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

scientific article published in 2016

Functional innovation from changes in protein domains and their combinations

scientific article published on 13 June 2016

Functional site plasticity in domain superfamilies

scientific article published on 14 March 2013

GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains

scientific article

Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression

scientific article published on 19 August 2015

Gene3D: Extensive prediction of globular domains in proteins

scientific article published on 3 November 2017

Gene3D: Extensive prediction of globular domains in proteins

scientific article published on 29 November 2017

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis

scientific article

Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

scientific article published in December 2011

Gene3D: comprehensive structural and functional annotation of genomes

scientific article

Gene3D: merging structure and function for a Thousand genomes

scientific article

Gene3D: modelling protein structure, function and evolution

scientific 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 analysis: Assigning protein coding regions to three-dimensional structures

scientific article published on April 1999

Genome-wide RNA-Sequencing analysis identifies a distinct fibrosis gene signature in the conjunctiva after glaucoma surgery

scientific article

Genome-wide transcriptional profiling of skin and dorsal root ganglia after ultraviolet-B-induced inflammation

scientific article

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

scientific article

Genome3D: exploiting structure to help users understand their sequences

scientific article

Genomewide function conservation and phylogeny in the Herpesviridae

scientific article published on January 2001

Genomic insights into evolution

scientific article

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing

scientific article

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing

scientific article

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing

scientific article published on 24 March 2016

ISPIDER Central: an integrated database web-server for proteomics

scientific article published on 25 April 2008

Identification and classification of protein fold families

scientific article

Identification and distribution of protein families in 120 completed genomes using Gene3D.

scientific article published in May 2005

Identification of new herpesvirus gene homologs in the human genome

scientific article published on November 2002

Identifying and characterising key alternative splicing events in Drosophila development

scientific article published on 16 August 2015

Inferring function using patterns of native disorder in proteins

scientific article

InterPro in 2011: new developments in the family and domain prediction database

scientific article

InterPro in 2011: new developments in the family and domain prediction database

scientific article published on 19 May 2012

InterPro in 2017-beyond protein family and domain annotations

scientific article

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

article by Alex Mitchell et al published 6 November 2018 in Nucleic Acids Research

InterPro: the integrative protein signature database

scientific article

Interactions between estrogen and EGF in uterine growth and function.

scientific article published in January 1987

Landscape of activating cancer mutations in FGFR kinases and their differential responses to inhibitors in clinical use. ⬇️

scientific article

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

scientific article published on 13 November 2015

LigASite--a database of biologically relevant binding sites in proteins with known apo-structures

scientific article published on 11 October 2007

Low-density lipoprotein receptor gene familial hypercholesterolemia variant database: update and pathological assessment

scientific article

Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone

scientific article

Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma

scientific article

Microeconomic principles explain an optimal genome size in bacteria

scientific article published in January 2005

Multiple protein structure alignment

scientific article

New developments in the InterPro database

scientific article

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

scientific article

Nonalcohol-related use disorders in geropsychiatric patients

scientific article

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases

scientific article

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)

Outcome of a workshop on archiving structural models of biological macromolecules

scientific article

Outcome of psychiatric hospitalization for very low-functioning demented patients

scientific article

PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources

scientific article

PROTEIN FAMILIES AND THEIR EVOLUTION—A STRUCTURAL PERSPECTIVE

scientific article

PSI-2: structural genomics to cover protein domain family space.

scientific article

PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations

scientific article published on 11 September 2013

Plasticity of enzyme active sites

scientific article

Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations

scientific article

Predicting protein function from sequence and structure

scientific article published on December 2007

Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes

scientific article

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

scientific article

Progress towards mapping the universe of protein folds

scientific article

Protein CoAlation and antioxidant function of Coenzyme A in prokaryotic cells

scientific article published on 6 April 2018

Protein Structure Classification

Protein folds and functions

scientific article

Protein folds, functions and evolution

scientific article

Protein function annotation by homology-based inference

scientific article (publication date: 2 February 2009)

Protein function annotation using protein domain family resources

scientific article published on October 2015

Protein function prediction using domain families ⬇️

scientific article published on February 28, 2013

Protein function prediction--the power of multiplicity

scientific article published on 27 February 2009

Protein structure alignment

scientific article

Protein structure and function analyses to understand the implication of mutually exclusive splicing

Protein superfamilies and domain superfolds

scientific article (publication date: 15 December 1994)

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

scientific article

Quantifying the similarities within fold space

scientific article

ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data

scientific article

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

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

scientific article

Review: what can structural classifications reveal about protein evolution?

scientific article

Rigid-body Ligand Recognition Drives Cytotoxic T-lymphocyte Antigen 4 (CTLA-4) Receptor Triggering

scientific article

SARS-CoV-2 spike protein predicted to form stable complexes with host receptor protein orthologues from mammals

scientific article published on 02 May 2020

SSAP: sequential structure alignment program for protein structure comparison

scientific article

Sensory, psychological, and metabolic dysfunction in HIV-associated peripheral neuropathy: A cross-sectional deep profiling study

scientific article

Sequence and structural differences between enzyme and nonenzyme homologs

scientific article published in October 2002

Sequences and topology

Shared structural motif in proteins

scientific article published in Nature

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.

scientific article published on 27 January 2014

Stress induces remodelling of yeast interaction and co-expression networks

scientific article published on 7 March 2013

Structural and Functional View of Polypharmacology

Structural diversity of domain superfamilies in the CATH database

scientific article

Structural genomics is the largest contributor of novel structural leverage

scientific article published on 05 February 2009

Structural insights into multi-protein communication systems

scientific article published in June 2012

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

scientific article published on October 1995

Survey of current protein family databases and their application in comparative, structural and functional genomics

scientific article

Systematic computational prediction of protein interaction networks

scientific article published on 13 May 2011

Systems biology approaches to finding novel pain mediators

scientific article published on 11 October 2012

Target selection and determination of function in structural genomics

scientific article

Target selection for structural genomics of infectious diseases

scientific article published on January 2014

Target selection for structural genomics: an overview

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

The Classification of Protein Domains

scientific article published on January 2017

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences

scientific article

The InterPro protein families database: the classification resource after 15 years

scientific article

The Pain in Neuropathy Study (PiNS): a cross-sectional observational study determining the somatosensory phenotype of painful and painless diabetic neuropathy

scientific article published on May 2016

The classification of protein domains

scientific article

The evolution of protein functions and networks: a family-centric approach

scientific article published in August 2009

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)

Tolerability and effectiveness of atypical antipsychotics in male geriatric inpatients

scientific article

Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint

scientific article

Towards fully automated structure-based function prediction in structural genomics: a case study

scientific article

Tracking dynamic changes in Alzheimer's disease brain proteome reveals ageing-independent damage in Drosophila

scholarly article published 19 December 2018

Transient protein-protein interactions: structural, functional, and network properties

scientific article published on October 2010

Transmission of SARS-CoV-2 from humans to animals and potential host adaptation

scientific article published on 27 May 2022

Trimethylaminuria and a human FMO3 mutation database

scientific article

Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology

scientific article

Understanding enzyme function evolution from a computational perspective

scientific article published on 7 September 2017

Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis ⬇️

scientific article published on 25 October 2017

Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models.

scientific article

Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.

scientific article

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

scientific article

VIDA: a virus database system for the organization of animal virus genome open reading frames

scientific article

VarSite: Disease variants and protein structure

scientific article published on 27 October 2019

Yeast cytochrome c oxidase: a model system to study mitochondrial forms of the haem-copper oxidase superfamily

scientific article published on 07 September 2011

Paulina is supported by:

About Paulina

Help