Published in BMC Evol Biol on September 09, 2008
Cholesterol, the central lipid of mammalian cells. Curr Opin Cell Biol (2010) 1.54
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. J Biol Chem (2011) 1.39
The conservation and evolutionary modularity of metabolism. Genome Biol (2009) 1.24
Origins of specificity and promiscuity in metabolic networks. J Biol Chem (2011) 0.99
Evolutionary constraints permeate large metabolic networks. BMC Evol Biol (2009) 0.95
Impact of constitutional copy number variants on biological pathway evolution. BMC Evol Biol (2013) 0.81
Evolution of domain architectures and catalytic functions of enzymes in metabolic systems. Genome Biol Evol (2012) 0.77
Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. BMC Evol Biol (2011) 0.76
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
The KEGG databases at GenomeNet. Nucleic Acids Res (2002) 33.68
The genome sequence of Schizosaccharomyces pombe. Nature (2002) 14.26
Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem (2004) 8.80
Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol (2001) 6.63
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol (2000) 4.75
Metabolic databases. Trends Biochem Sci (1998) 4.04
History of the enzyme nomenclature system. Bioinformatics (2000) 3.90
Practical limits of function prediction. Proteins (2000) 3.81
Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet (2002) 3.49
The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res (2006) 2.45
BioLayout(Java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics (2005) 2.26
The phylogenetic extent of metabolic enzymes and pathways. Genome Res (2003) 1.92
Universal protein families and the functional content of the last universal common ancestor. J Mol Evol (1999) 1.77
Molecular evolution of biomembranes: structural equivalents and phylogenetic precursors of sterols. Proc Natl Acad Sci U S A (1979) 1.67
Importance of glycosidases in mammalian glycoprotein biosynthesis. Biochim Biophys Acta (1999) 1.61
The selective cause of an ancient adaptation. Science (2005) 1.45
Structure, organization, and function of glycosphingolipids in membrane. Curr Opin Hematol (2003) 1.39
The humanization of N-glycosylation pathways in yeast. Nat Rev Microbiol (2005) 1.38
Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins. Genome Biol (2005) 1.33
Biosynthesis and degradation of mammalian glycosphingolipids. Philos Trans R Soc Lond B Biol Sci (2003) 1.29
Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics (2006) 1.23
The joys of HexNAc. The synthesis and function of N- and O-glycan branches. Glycoconj J (2001) 1.23
Origin of multicellular eukaryotes - insights from proteome comparisons. Curr Opin Genet Dev (1999) 1.14
The complement of enzymatic sets in different species. J Mol Biol (2005) 1.10
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. BMC Bioinformatics (2006) 1.00
Analysis of phenetic trees based on metabolic capabilites across the three domains of life. J Mol Biol (2004) 0.99
Evolution of metabolic networks by gain and loss of enzymatic reaction in eukaryotes. Gene (2005) 0.86
Evolution of multicellularity in Metazoa: comparative analysis of the subcellular localization of proteins in Saccharomyces, Drosophila and Caenorhabditis. Cell Biol Int (2004) 0.78
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
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res (2005) 5.79
Analysis of catalytic residues in enzyme active sites. J Mol Biol (2002) 4.90
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
Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics (2002) 4.12
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
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
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
Detection of functional modules from protein interaction networks. Proteins (2004) 3.08
Metal ions in biological catalysis: from enzyme databases to general principles. J Biol Inorg Chem (2008) 2.87
Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res (2004) 2.86
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
Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol (2007) 2.73
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics (2003) 2.70
Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res (2004) 2.66
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 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
The balance of driving forces during genome evolution in prokaryotes. Genome Res (2003) 2.39
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
The net of life: reconstructing the microbial phylogenetic network. Genome Res (2005) 2.31
Protein families and TRIBES in genome sequence space. Nucleic Acids Res (2003) 2.27
BioLayout(Java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics (2005) 2.26
Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol (2005) 2.22
Evolutionary conservation of regulated longevity assurance mechanisms. Genome Biol (2007) 2.19
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
Integrating biological data through the genome. Hum Mol Genet (2006) 2.12
Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A (2003) 2.08
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
The phylogenetic extent of metabolic enzymes and pathways. Genome Res (2003) 1.92
Using a neural network and spatial clustering to predict the location of active sites in enzymes. J Mol Biol (2003) 1.88
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
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
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics (2003) 1.77
Myriads of protein families, and still counting. Genome Biol (2003) 1.75
Plasticity of enzyme active sites. Trends Biochem Sci (2002) 1.75
Transcription regulation and environmental adaptation in bacteria. Trends Microbiol (2003) 1.63
Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res (2005) 1.61
Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J Biol Chem (2003) 1.61
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res (2006) 1.57
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
DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO. Mol Syst Biol (2010) 1.48
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
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res (2013) 1.42
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
MagicMatch--cross-referencing sequence identifiers across databases. Bioinformatics (2005) 1.34
Highly consistent patterns for inherited human diseases at the molecular level. Bioinformatics (2005) 1.33
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
Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins. Genome Biol (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
MACiE: a database of enzyme reaction mechanisms. Bioinformatics (2005) 1.32
An exponential core in the heart of the yeast protein interaction network. Mol Biol Evol (2004) 1.31
Structural and functional properties of genes involved in human cancer. BMC Genomics (2006) 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
The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Res (2003) 1.28
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
A structure-based anatomy of the E.coli metabolome. J Mol Biol (2003) 1.27
Percolation of annotation errors through hierarchically structured protein sequence databases. Math Biosci (2005) 1.27
Towards fully automated structure-based function prediction in structural genomics: a case study. J Mol Biol (2007) 1.26
Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep (2005) 1.25
Functional evolution of the yeast protein interaction network. Mol Biol Evol (2004) 1.25
Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J Mol Biol (2007) 1.24
GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics (2003) 1.23
Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics (2009) 1.23
Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J Mol Biol (2002) 1.22
Ligand selectivity and competition between enzymes in silico. Nat Biotechnol (2004) 1.22
ELIXIR: a distributed infrastructure for European biological data. Trends Biotechnol (2012) 1.21
Wavelet transforms for the characterization and detection of repeating motifs. J Mol Biol (2002) 1.21
Understanding the molecular machinery of genetics through 3D structures. Nat Rev Genet (2008) 1.20