Published in Annu Rev Biochem on January 01, 2005
Protein sectors: evolutionary units of three-dimensional structure. Cell (2009) 3.76
The evolutionary origin of orphan genes. Nat Rev Genet (2011) 2.98
MSDmotif: exploring protein sites and motifs. BMC Bioinformatics (2008) 2.48
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A (2008) 2.44
Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus. Nat Immunol (2006) 1.92
Evolution of protein domain promiscuity in eukaryotes. Genome Res (2008) 1.82
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev (2015) 1.74
ASH structure alignment package: sensitivity and selectivity in domain classification. BMC Bioinformatics (2007) 1.73
Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci U S A (2010) 1.71
Multicopy suppression underpins metabolic evolvability. Mol Biol Evol (2007) 1.63
The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. Structure (2009) 1.62
Functional diversity of ankyrin repeats in microbial proteins. Trends Microbiol (2009) 1.58
Iron-sulfur protein folds, iron-sulfur chemistry, and evolution. J Biol Inorg Chem (2007) 1.52
High-throughput crystallography for structural genomics. Curr Opin Struct Biol (2009) 1.44
Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces. BMC Struct Biol (2016) 1.39
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA (2008) 1.39
Structural and functional constraints in the evolution of protein families. Nat Rev Mol Cell Biol (2009) 1.35
On homology searches by protein Blast and the characterization of the age of genes. BMC Evol Biol (2007) 1.28
Binding ligand prediction for proteins using partial matching of local surface patches. Int J Mol Sci (2010) 1.23
Reductive evolution of proteomes and protein structures. Proc Natl Acad Sci U S A (2011) 1.18
Development of a heme protein structure-electrochemical function database. Nucleic Acids Res (2007) 1.18
Structural genomics: keeping up with expanding knowledge of the protein universe. Curr Opin Struct Biol (2007) 1.17
Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLoS Genet (2008) 1.14
Real-time ligand binding pocket database search using local surface descriptors. Proteins (2010) 1.12
Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'-5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch. Biol Direct (2008) 1.11
Evolution of the arginase fold and functional diversity. Cell Mol Life Sci (2008) 1.09
Evidence for the adaptation of protein pH-dependence to subcellular pH. BMC Biol (2009) 1.09
Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles. Protein Sci (2008) 1.08
What makes species unique? The contribution of proteins with obscure features. Genome Biol (2006) 1.08
Ortholog identification in the presence of domain architecture rearrangement. Brief Bioinform (2011) 1.08
Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol (2009) 1.07
Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS One (2009) 1.06
Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids. Nature (2013) 1.06
A galaxy of folds. Protein Sci (2010) 1.05
Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors. BMC Struct Biol (2009) 1.04
The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Comput Biol (2011) 1.03
Modeling protein network evolution under genome duplication and domain shuffling. BMC Syst Biol (2007) 1.03
'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Res (2006) 1.01
Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction. J Am Chem Soc (2007) 0.98
Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins. J Biol Chem (2010) 0.96
A vocabulary of ancient peptides at the origin of folded proteins. Elife (2015) 0.95
Protein domain organisation: adding order. BMC Bioinformatics (2009) 0.91
The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease. Structure (2009) 0.91
Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes. BMC Genomics (2008) 0.91
Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A (2013) 0.91
Why reinvent the wheel? Building new proteins based on ready-made parts. Protein Sci (2016) 0.88
Predicting prokaryotic ecological niches using genome sequence analysis. PLoS One (2007) 0.87
Universal features in the genome-level evolution of protein domains. Genome Biol (2009) 0.85
Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philos Trans R Soc Lond B Biol Sci (2006) 0.85
Molecular analysis of spring viraemia of carp virus in China: a fatal aquatic viral disease that might spread in East Asian. PLoS One (2009) 0.85
Intramolecular arrangement of sensor and regulator overcomes relaxed specificity in hybrid two-component systems. Proc Natl Acad Sci U S A (2012) 0.84
Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes. Funct Integr Genomics (2009) 0.83
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. BMC Evol Biol (2006) 0.82
The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma. BMC Med Genomics (2009) 0.82
Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization. Proc Natl Acad Sci U S A (2010) 0.81
Multiple interactions of the intrinsically disordered region between the helicase and nuclease domains of the archaeal Hef protein. J Biol Chem (2014) 0.81
Flagellated algae protein evolution suggests the prevalence of lineage-specific rules governing evolutionary rates of eukaryotic proteins. Genome Biol Evol (2013) 0.81
Evolution of S-domain receptor-like kinases in land plants and origination of S-locus receptor kinases in Brassicaceae. BMC Evol Biol (2013) 0.79
A conserved helical capping hydrogen bond in PAS domains controls signaling kinetics in the superfamily prototype photoactive yellow protein. J Am Chem Soc (2010) 0.79
Structural and functional study of YER067W, a new protein involved in yeast metabolism control and drug resistance. PLoS One (2010) 0.79
Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach. PLoS One (2012) 0.79
Origin of a folded repeat protein from an intrinsically disordered ancestor. Elife (2016) 0.78
On the detection of functionally coherent groups of protein domains with an extension to protein annotation. BMC Bioinformatics (2007) 0.78
Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks. PLoS One (2011) 0.78
Preservation of protein clefts in comparative models. BMC Struct Biol (2008) 0.78
Linking fold, function and phylogeny: a comparative genomics view on protein (domain) evolution. Curr Genomics (2008) 0.78
The nature of protein domain evolution: shaping the interaction network. Curr Genomics (2010) 0.77
The architectural design of networks of protein domain architectures. Biol Lett (2013) 0.77
Caenorhabditis elegans NONO-1: Insights into DBHS protein structure, architecture, and function. Protein Sci (2015) 0.77
Protein cold adaptation strategy via a unique seven-amino acid domain in the icefish (Chionodraco hamatus) PEPT1 transporter. Proc Natl Acad Sci U S A (2013) 0.76
PDB-Explorer: a web-based interactive map of the protein data bank in shape space. BMC Bioinformatics (2015) 0.76
The history of the CATH structural classification of protein domains. Biochimie (2015) 0.76
Stylus: a system for evolutionary experimentation based on a protein/proteome model with non-arbitrary functional constraints. PLoS One (2008) 0.75
Genome-wide detection of hybrid genes with multiple components in human. BMC Res Notes (2009) 0.75
Overcoming sequence misalignments with weighted structural superposition. Proteins (2012) 0.75
Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers. Nucleic Acids Res (2014) 0.75
Convergence of domain architecture, structure and ligand affinity in animal and plant RNA-binding proteins. Mol Biol Evol (2017) 0.75
Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals. BMC Genomics (2017) 0.75
Improved performance of sequence search algorithms in remote homology detection. F1000Res (2013) 0.75
Census of prokaryotic senses. J Bacteriol (2006) 0.75
Compressing proteomes: the relevance of medium range correlations. EURASIP J Bioinform Syst Biol (2007) 0.75
Molecular evolution of threonine dehydratase in bacteria. PLoS One (2013) 0.75
Random sequences are an abundant source of bioactive RNAs or peptides. Nat Ecol Evol (2017) 0.75
Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements. Sci Rep (2017) 0.75
Molecular Phylogenetics and the Perennial Problem of Homology. J Mol Evol (2016) 0.75
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
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
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
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
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol (2002) 2.52
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
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
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
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
Plasticity of enzyme active sites. Trends Biochem Sci (2002) 1.75
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
The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics (2002) 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
Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol (2009) 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
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
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
Ligand selectivity and competition between enzymes in silico. Nat Biotechnol (2004) 1.22
Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J Mol Biol (2002) 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
Morphological aspects of oligomeric protein structures. Prog Biophys Mol Biol (2005) 1.20
Heme proteins--diversity in structural characteristics, function, and folding. Proteins (2010) 1.19
PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Res (2007) 1.18
Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory. Proteins (2002) 1.18
The structural basis of allosteric regulation in proteins. FEBS Lett (2009) 1.18
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Res (2011) 1.17
Understanding nature's catalytic toolkit. Trends Biochem Sci (2005) 1.17
Protein superfamily evolution and the last universal common ancestor (LUCA). J Mol Evol (2006) 1.17
Conformational diversity of ligands bound to proteins. J Mol Biol (2005) 1.16
On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins (2010) 1.12
Correcting for sequence biases in present/absent calls. Genome Biol (2007) 1.12
Missing in action: enzyme functional annotations in biological databases. Nat Chem Biol (2009) 1.11
The complement of enzymatic sets in different species. J Mol Biol (2005) 1.10
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PLoS Comput Biol (2012) 1.09
WSsas: a web service for the annotation of functional residues through structural homologues. Bioinformatics (2009) 1.08
Evolution of enzymes and pathways for the biosynthesis of cofactors. Nat Prod Rep (2007) 1.07
Estimation and correction of non-specific binding in a large-scale spike-in experiment. Genome Biol (2007) 1.07
Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res (2003) 1.07
Structural analysis of metal sites in proteins: non-heme iron sites as a case study. J Mol Biol (2009) 1.06
Target selection and determination of function in structural genomics. IUBMB Life (2003) 1.05
Inferring protein function from structure. Methods Biochem Anal (2003) 1.04
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. Bioinformatics (2007) 1.03
Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv. Aging Cell (2013) 1.02
Toward the detection and validation of repeats in protein structure. Proteins (2004) 1.02
The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics (2010) 1.01
Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk. PLoS Genet (2010) 1.01
Cognate ligand domain mapping for enzymes. J Mol Biol (2006) 1.00
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network. PLoS Comput Biol (2007) 1.00
Microeconomic principles explain an optimal genome size in bacteria. Trends Genet (2005) 0.99
SCOPEC: a database of protein catalytic domains. Bioinformatics (2004) 0.98
The chemistry of protein catalysis. J Mol Biol (2007) 0.98
A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks. Proteins (2003) 0.98
Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models. Protein Eng Des Sel (2004) 0.97
An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure. J Mol Biol (2006) 0.97