Published in Genome Biol on June 29, 2005
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Functional protein divergence in the evolution of Homo sapiens. Genome Biol (2008) 1.32
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Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
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Ribosomal protein S6 kinase 1 signaling regulates mammalian life span. Science (2009) 7.80
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res (2004) 7.21
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A promoter-level mammalian expression atlas. Nature (2014) 6.25
ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res (2005) 5.79
Interleukin-2 gene variation impairs regulatory T cell function and causes autoimmunity. Nat Genet (2007) 5.68
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Predicting protein function from sequence and structural data. Curr Opin Struct Biol (2005) 4.31
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res (2005) 4.20
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol (2002) 3.88
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res (2007) 3.84
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res (2006) 3.84
Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice. FASEB J (2007) 3.83
Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol (2003) 3.72
Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway. Cell (2013) 3.49
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res (2012) 3.36
Catalysing new reactions during evolution: economy of residues and mechanism. J Mol Biol (2003) 3.35
Diversity of protein-protein interactions. EMBO J (2003) 3.35
A CD8+ T cell transcription signature predicts prognosis in autoimmune disease. Nat Med (2010) 2.88
Metal ions in biological catalysis: from enzyme databases to general principles. J Biol Inorg Chem (2008) 2.87
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol (2009) 2.82
Protein promiscuity and its implications for biotechnology. Nat Biotechnol (2009) 2.78
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics (2003) 2.70
Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc (2009) 2.66
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol (2002) 2.52
Protein families and their evolution-a structural perspective. Annu Rev Biochem (2005) 2.45
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res (2003) 2.37
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33
Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol (2005) 2.22
Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. Nat Genet (2003) 2.21
Evolutionary conservation of regulated longevity assurance mechanisms. Genome Biol (2007) 2.19
Positional cloning of a novel gene influencing asthma from chromosome 2q14. Nat Genet (2003) 2.16
A method for localizing ligand binding pockets in protein structures. Proteins (2006) 2.16
Protein function prediction using local 3D templates. J Mol Biol (2005) 2.13
Copy number of FCGR3B, which is associated with systemic lupus erythematosus, correlates with protein expression and immune complex uptake. J Exp Med (2008) 2.13
Integrating biological data through the genome. Hum Mol Genet (2006) 2.12
Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein. Hum Mutat (2002) 1.99
Evolution of protein superfamilies and bacterial genome size. J Mol Biol (2004) 1.97
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics (2005) 1.97
PDBsum additions. Nucleic Acids Res (2013) 1.94
Small Molecule Subgraph Detector (SMSD) toolkit. J Cheminform (2009) 1.94
Genomic DNA k-mer spectra: models and modalities. Genome Biol (2009) 1.92
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015) 1.91
Using a neural network and spatial clustering to predict the location of active sites in enzymes. J Mol Biol (2003) 1.88
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res (2006) 1.87
Searching for functional sites in protein structures. Curr Opin Chem Biol (2004) 1.84
Shape variation in protein binding pockets and their ligands. J Mol Biol (2007) 1.83
Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res (2003) 1.82
Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol (2005) 1.81
The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. Chem Biol Interact (2008) 1.77
Plasticity of enzyme active sites. Trends Biochem Sci (2002) 1.75
Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: the NOD model of type 1 diabetes. Genome Res (2002) 1.68
Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J Biol Chem (2003) 1.61
Fine mapping, gene content, comparative sequencing, and expression analyses support Ctla4 and Nramp1 as candidates for Idd5.1 and Idd5.2 in the nonobese diabetic mouse. J Immunol (2004) 1.59
Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol (2015) 1.58
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res (2006) 1.57
Analysis of a wild mouse promoter variant reveals a novel role for FcγRIIb in the control of the germinal center and autoimmunity. J Exp Med (2012) 1.55
Lactobacillus acidophilus alleviates platelet-activating factor-induced inflammatory responses in human intestinal epithelial cells. PLoS One (2013) 1.54
From protein structure to biochemical function? J Struct Funct Genomics (2003) 1.54
Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Res (2004) 1.50
Molecular basis of inherited diseases: a structural perspective. Trends Genet (2003) 1.49
A logic-based diagram of signalling pathways central to macrophage activation. BMC Syst Biol (2008) 1.49
DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO. Mol Syst Biol (2010) 1.48
Gene expression profiling of CD8+ T cells predicts prognosis in patients with Crohn disease and ulcerative colitis. J Clin Invest (2011) 1.47
Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice. Physiol Genomics (2006) 1.47
Pathway evolution, structurally speaking. Curr Opin Struct Biol (2002) 1.44
Distinct cell-specific control of autoimmunity and infection by FcgammaRIIb. J Exp Med (2008) 1.43
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res (2013) 1.42
A defunctioning polymorphism in FCGR2B is associated with protection against malaria but susceptibility to systemic lupus erythematosus. Proc Natl Acad Sci U S A (2010) 1.41
Efficient inhibition of miR-155 function in vivo by peptide nucleic acids. Nucleic Acids Res (2010) 1.41
Copy number, linkage disequilibrium and disease association in the FCGR locus. Hum Mol Genet (2010) 1.41
An oligonucleotide microarray for transcriptome analysis of Schistosoma mansoni and its application/use to investigate gender-associated gene expression. Mol Biochem Parasitol (2005) 1.36
The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions. PLoS Genet (2010) 1.36
A bioinformatician's view of the metabolome. Bioessays (2006) 1.35
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Comput Biol (2009) 1.35
Sequence and structural differences between enzyme and nonenzyme homologs. Structure (2002) 1.34
The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics (2002) 1.33
Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol (2009) 1.33
The genes induced by signal transducer and activators of transcription (STAT)3 and STAT5 in mammary epithelial cells define the roles of these STATs in mammary development. Mol Endocrinol (2005) 1.33
Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res (2003) 1.32
Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling. Mol Syst Biol (2011) 1.32
Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations. Immunobiology (2010) 1.32
A missense mutation disrupting a dibasic prohormone processing site in pro-opiomelanocortin (POMC) increases susceptibility to early-onset obesity through a novel molecular mechanism. Hum Mol Genet (2002) 1.32
MACiE: a database of enzyme reaction mechanisms. Bioinformatics (2005) 1.32
Carrageenan induces interleukin-8 production through distinct Bcl10 pathway in normal human colonic epithelial cells. Am J Physiol Gastrointest Liver Physiol (2006) 1.29
Genetic control of autoimmunity: protection from diabetes, but spontaneous autoimmune biliary disease in a nonobese diabetic congenic strain. J Immunol (2004) 1.29
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome Res (2002) 1.29
Effective function annotation through catalytic residue conservation. Proc Natl Acad Sci U S A (2005) 1.28
A structure-based anatomy of the E.coli metabolome. J Mol Biol (2003) 1.27
Towards fully automated structure-based function prediction in structural genomics: a case study. J Mol Biol (2007) 1.26
Determination and validation of principal gene products. Bioinformatics (2007) 1.25
Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J Mol Biol (2007) 1.24
Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics (2009) 1.23