Published in J Mol Biol on December 20, 2005
Protein promiscuity and its implications for biotechnology. Nat Biotechnol (2009) 2.78
The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol (2010) 2.07
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics (2008) 1.23
Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites. BMC Struct Biol (2008) 1.09
Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. Biophys J (2009) 0.99
Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. Protein Sci (2008) 0.99
Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. Genome Biol (2007) 0.98
Protein pockets: inventory, shape, and comparison. J Chem Inf Model (2010) 0.88
FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Res (2013) 0.87
A study on the flexibility of enzyme active sites. BMC Bioinformatics (2011) 0.86
Representation of target-bound drugs by computed conformers: implications for conformational libraries. BMC Bioinformatics (2006) 0.84
The natural history of biocatalytic mechanisms. PLoS Comput Biol (2014) 0.83
Self-complementarity within proteins: bridging the gap between binding and folding. Biophys J (2012) 0.82
Assisted assignment of ligands corresponding to unknown electron density. J Struct Funct Genomics (2010) 0.81
A global optimization algorithm for protein surface alignment. BMC Bioinformatics (2010) 0.79
Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. Front Mol Biosci (2015) 0.75
Estimation of the protein-ligand interaction energy for model building and validation. Acta Crystallogr D Struct Biol (2017) 0.75
Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. Nucleic Acids Res (2013) 0.75
Electron Paramagnetic Resonance and Electron Spin Echo Studies of Co(2+) Coordination by Nicotinamide Adenine Dinucleotide (NAD(+)) in Water Solution. Appl Magn Reson (2013) 0.75
Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. J Mol Recognit (2017) 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
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
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
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
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
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
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
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
Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res (2003) 1.07
Estimation and correction of non-specific binding in a large-scale spike-in experiment. Genome Biol (2007) 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
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network. PLoS Comput Biol (2007) 1.00
Cognate ligand domain mapping for enzymes. J Mol Biol (2006) 1.00
Microeconomic principles explain an optimal genome size in bacteria. Trends Genet (2005) 0.99
A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks. Proteins (2003) 0.98
SCOPEC: a database of protein catalytic domains. Bioinformatics (2004) 0.98
The chemistry of protein catalysis. J Mol Biol (2007) 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