Protein promiscuity and its implications for biotechnology.

Predicting new molecular targets for known drugs. Nature (2009) 9.71

The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol (2010) 2.07

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev (2015) 1.74

The impact of multifunctional genes on "guilt by association" analysis. PLoS One (2011) 1.69

Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc Natl Acad Sci U S A (2010) 1.65

Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome--clozapine-induced agranulocytosis as a case study. PLoS Comput Biol (2011) 1.26

Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol (2011) 1.25

Hub promiscuity in protein-protein interaction networks. Int J Mol Sci (2010) 1.22

Further developments towards a genome-scale metabolic model of yeast. BMC Syst Biol (2010) 1.20

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci U S A (2012) 1.13

Missing in action: enzyme functional annotations in biological databases. Nat Chem Biol (2009) 1.11

Extending biochemical databases by metabolomic surveys. J Biol Chem (2011) 1.09

HDAC8 substrates: Histones and beyond. Biopolymers (2013) 1.08

Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface (2014) 1.08

A comprehensive survey of small-molecule binding pockets in proteins. PLoS Comput Biol (2013) 1.04

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med (2013) 1.04

Enzyme promiscuity: engine of evolutionary innovation. J Biol Chem (2014) 1.02

MultitaskProtDB: a database of multitasking proteins. Nucleic Acids Res (2013) 1.02

How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Front Pharmacol (2014) 1.00

Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network. Protein Sci (2010) 0.99

MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. Nucleic Acids Res (2009) 0.98

Exploring functional roles of multibinding protein interfaces. Protein Sci (2009) 0.97

Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. Nat Commun (2015) 0.97

Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation. Protein Sci (2010) 0.96

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PLoS One (2013) 0.94

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Mol Syst Biol (2012) 0.94

Viral-host interactions that control HIV-1 transcriptional elongation. Chem Rev (2013) 0.93

Signal transduction networks in cancer: quantitative parameters influence network topology. Cancer Res (2010) 0.91

Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. Bioinformatics (2011) 0.91

Hydrophobicity and charge shape cellular metabolite concentrations. PLoS Comput Biol (2011) 0.91

Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase. PLoS One (2011) 0.90

Substrate-driven mapping of the degradome by comparison of sequence logos. PLoS Comput Biol (2013) 0.90

Multifunctional enzymes in archaea: promiscuity and moonlight. Extremophiles (2013) 0.89

Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. J Biol Chem (2012) 0.89

Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys (2013) 0.89

A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity. PLoS One (2012) 0.89

Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers. Chembiochem (2010) 0.88

Protein pockets: inventory, shape, and comparison. J Chem Inf Model (2010) 0.88

Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way. PLoS Comput Biol (2010) 0.87

Identification and characterization of carprofen as a multitarget fatty acid amide hydrolase/cyclooxygenase inhibitor. J Med Chem (2012) 0.87

Intrinsic disorder and protein multibinding in domain, terminal, and linker regions. Mol Biosyst (2010) 0.85

Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat Commun (2014) 0.84

Metabolite and reaction inference based on enzyme specificities. Bioinformatics (2009) 0.84

Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily. J Am Chem Soc (2013) 0.84

Development of antibody arrays for monoclonal antibody Higher Order Structure analysis. Front Pharmacol (2013) 0.83

Multiple conformers in active site of human dihydrofolate reductase F31R/Q35E double mutant suggest structural basis for methotrexate resistance. J Biol Chem (2009) 0.83

Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin. PLoS Comput Biol (2013) 0.82

Proteins from an unevolved library of de novo designed sequences bind a range of small molecules. ACS Synth Biol (2012) 0.82

Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III. Proc Natl Acad Sci U S A (2012) 0.82

Identification and analysis of residues contained on beta --> alpha loops of the dual-substrate (beta alpha)8 phosphoribosyl isomerase A specific for its phosphoribosyl anthranilate isomerase activity. Protein Sci (2010) 0.82

XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res (2014) 0.81

The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network. PLoS One (2011) 0.81

Modeling for (physical) biologists: an introduction to the rule-based approach. Phys Biol (2015) 0.81

(19)F NMR reveals multiple conformations at the dimer interface of the nonstructural protein 1 effector domain from influenza A virus. Structure (2014) 0.81

Characterizing protein domain associations by Small-molecule ligand binding. J Proteome Sci Comput Biol (2012) 0.80

An attempt to construct a (general) mathematical framework to model biological "context-dependence". Syst Synth Biol (2013) 0.80

Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. PLoS Comput Biol (2013) 0.80

Handicap-Recover Evolution Leads to a Chemically Versatile, Nucleophile-Permissive Protease. Chembiochem (2015) 0.80

Importance of consensus region of multiple-ligand templates in a virtual screening method. Biophys Physicobiol (2016) 0.80

A genome scale overexpression screen to reveal drug activity in human cells. Genome Med (2014) 0.80

The coupling of pathways and processes through shared components. BMC Syst Biol (2011) 0.80

Determination of minimal transcriptional signatures of compounds for target prediction. EURASIP J Bioinform Syst Biol (2012) 0.80

Designing allostery-inspired response in mechanical networks. Proc Natl Acad Sci U S A (2017) 0.79

Heme binding properties of glyceraldehyde-3-phosphate dehydrogenase. Biochemistry (2012) 0.79

Probing the mutational interplay between primary and promiscuous protein functions: a computational-experimental approach. PLoS Comput Biol (2012) 0.79

Structural and functional characterization of a multifunctional alanine-rich peptide analogue from Pleuronectes americanus. PLoS One (2012) 0.79

Targeting ligand-gated ion channels in neurology and psychiatry: is pharmacological promiscuity an obstacle or an opportunity? BMC Pharmacol (2010) 0.79

Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12. Sci Rep (2015) 0.79

Pyranose dehydrogenase ligand promiscuity: a generalized approach to simulate monosaccharide solvation, binding, and product formation. PLoS Comput Biol (2014) 0.79

Computational tools for rational protein engineering of aldolases. Comput Struct Biotechnol J (2012) 0.79

Substrate binding process and mechanistic functioning of type 1 11β-hydroxysteroid dehydrogenase from enhanced sampling methods. PLoS One (2011) 0.79

Achieving peptide binding specificity and promiscuity by loops: case of the forkhead-associated domain. PLoS One (2014) 0.78

Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics (2014) 0.78

Dynamic New World: Refining Our View of Protein Structure, Function and Evolution. Proteomes (2014) 0.77

Cofactor-mediated protein promiscuity. Nat Biotechnol (2009) 0.77

Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. Front Microbiol (2016) 0.77

Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. Biochemistry (2016) 0.77

Protease-catalysed direct asymmetric Mannich reaction in organic solvent. Sci Rep (2012) 0.77

Human casein alpha s1 (CSN1S1) skews in vitro differentiation of monocytes towards macrophages. BMC Immunol (2013) 0.77

Structural interpretation of protein-protein interaction network. BMC Struct Biol (2010) 0.77

From microbiology to cancer biology: the Rid protein family prevents cellular damage caused by endogenously generated reactive nitrogen species. Mol Microbiol (2015) 0.77

Cys-X scanning for expansion of active-site residues and modulation of catalytic functions in a glutathione transferase. J Biol Chem (2011) 0.77

Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae. PLoS One (2012) 0.77

Dual specificity of anti-CXCL10-CXCL9 antibodies is governed by structural mimicry. J Biol Chem (2011) 0.77

Bioinformatics and Moonlighting Proteins. Front Bioeng Biotechnol (2015) 0.77

Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12. Protein Sci (2013) 0.77

Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. Prog Biophys Mol Biol (2014) 0.76

Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophys J (2015) 0.76

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. Sci Signal (2016) 0.76

Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Nat Methods (2016) 0.76

Ingestion-controlling network: what's language got to do with it? Rev Neurosci (2010) 0.76

Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426. PLoS One (2015) 0.76

Improving chemical similarity ensemble approach in target prediction. J Cheminform (2016) 0.76

Biological messiness vs. biological genius: Mechanistic aspects and roles of protein promiscuity. J Steroid Biochem Mol Biol (2014) 0.76

Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. Sci Rep (2016) 0.76

The 'Tyranny of choices' in the ingestion-controlling network. Obes Facts (2009) 0.76

Motif mediated protein-protein interactions as drug targets. Cell Commun Signal (2016) 0.76

Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders. Schizophr Res Treatment (2016) 0.75

Structure and specificity of a permissive bacterial C-prenyltransferase. Nat Chem Biol (2017) 0.75

Chalcone Isomerase from Eubacterium ramulus Catalyzes the Ring Contraction of Flavanonols. J Bacteriol (2016) 0.75

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

The druggable genome. Nat Rev Drug Discov (2002) 13.61

Drug target identification using side-effect similarity. Science (2008) 9.24

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04

Enzyme recruitment in evolution of new function. Annu Rev Microbiol (1976) 6.95

Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol (2001) 6.63

Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol (2006) 5.92

New uses for old drugs. Nature (2007) 5.86

Protein stability promotes evolvability. Proc Natl Acad Sci U S A (2006) 5.73

The 'evolvability' of promiscuous protein functions. Nat Genet (2004) 5.41

Pyruvate kinase type M2 and its role in tumor growth and spreading. Semin Cancer Biol (2005) 5.25

Antibody multispecificity mediated by conformational diversity. Science (2003) 5.21

Moonlighting proteins. Trends Biochem Sci (1999) 4.53

Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition. Nat Struct Mol Biol (2004) 4.40

Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia. Nat Rev Drug Discov (2004) 4.31

Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem (2001) 4.17

From magic bullets to designed multiple ligands. Drug Discov Today (2004) 4.09

Practical limits of function prediction. Proteins (2000) 3.81

Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci U S A (2006) 3.74

Anatomy of the antibody molecule. Mol Immunol (1994) 3.65

Catalytic promiscuity and the evolution of new enzymatic activities. Chem Biol (1999) 3.54

Short-chain dehydrogenases/reductases (SDR): the 2002 update. Chem Biol Interact (2003) 3.46

Structural and catalytic diversity within the amidohydrolase superfamily. Biochemistry (2005) 3.34

Enzyme promiscuity: evolutionary and mechanistic aspects. Curr Opin Chem Biol (2006) 3.28

Molecular complexity and its impact on the probability of finding leads for drug discovery. J Chem Inf Comput Sci (2001) 3.24

Conformational diversity and protein evolution--a 60-year-old hypothesis revisited. Trends Biochem Sci (2003) 3.24

A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases. Proc Natl Acad Sci U S A (2007) 3.21

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci (2002) 3.01

The nuclear pregnane X receptor: a key regulator of xenobiotic metabolism. Endocr Rev (2002) 2.95

Implications of protein flexibility for drug discovery. Nat Rev Drug Discov (2003) 2.83

Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol (2004) 2.58

Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol (2003) 2.56

The generation of new protein functions by the combination of domains. Structure (2007) 2.51

Complementarity of structure ensembles in protein-protein binding. Structure (2004) 2.44

The small heat-shock protein alpha B-crystallin as candidate autoantigen in multiple sclerosis. Nature (1995) 2.44

Counting the zinc-proteins encoded in the human genome. J Proteome Res (2006) 2.38

Evolution of enzyme superfamilies. Curr Opin Chem Biol (2006) 2.30

Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys (2005) 2.18

Calmodulin's flexibility allows for promiscuity in its interactions with target proteins and peptides. Mol Biotechnol (2004) 2.14

Combinatorial and computational challenges for biocatalyst design. Nature (2001) 2.11

Purification and characterization of cytosolic aconitase from beef liver and its relationship to the iron-responsive element binding protein. Proc Natl Acad Sci U S A (1992) 2.06

Can we rationally design promiscuous drugs? Curr Opin Struct Biol (2006) 2.06

Robustness, evolvability, and neutrality. FEBS Lett (2005) 2.06

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Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem (2004) 2.04

Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response. Immunity (2006) 1.95

Directed enzyme evolution. Curr Opin Biotechnol (2001) 1.89

Predicting undesirable drug interactions with promiscuous proteins in silico. Drug Discov Today (2004) 1.79

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The pentafunctional arom enzyme of Saccharomyces cerevisiae is a mosaic of monofunctional domains. Biochem J (1987) 1.77

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Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha. Science (2003) 1.65

In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J Mol Biol (2001) 1.65

Multidrug efflux pumps and resistance: regulation and evolution. Curr Opin Microbiol (2003) 1.63

One pathway, many products. Nat Chem Biol (2007) 1.63

Crystal structure of the GpIbalpha-thrombin complex essential for platelet aggregation. Science (2003) 1.57

Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition. J Med Chem (2004) 1.57

Transition towards antigen-binding promiscuity of a monospecific antibody. Mol Immunol (2006) 1.54

Short-chain dehydrogenase/reductase (SDR) relationships: a large family with eight clusters common to human, animal, and plant genomes. Protein Sci (2002) 1.54

Single-gene disorders: what role could moonlighting enzymes play? Am J Hum Genet (2005) 1.52

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Directed evolution of a (beta alpha)8-barrel enzyme to catalyze related reactions in two different metabolic pathways. Proc Natl Acad Sci U S A (2000) 1.51

Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways. Angew Chem Int Ed Engl (2004) 1.47

G protein selectivity is regulated by multiple intracellular regions of GPCRs. Neurosignals (2003) 1.47

Improved biocatalysts by directed evolution and rational protein design. Curr Opin Chem Biol (2001) 1.39

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The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness. Protein Sci (2003) 1.38

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Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry (2003) 1.36

Moonlighting proteins in yeasts. Microbiol Mol Biol Rev (2008) 1.36

Promiscuous drugs compared to selective drugs (promiscuity can be a virtue). BMC Clin Pharmacol (2005) 1.34

Protein engineering 20 years on. Nat Rev Mol Cell Biol (2002) 1.34

Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. J Am Chem Soc (2006) 1.27

Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar. Structure (1993) 1.26

Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci U S A (2006) 1.26

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Ligand selectivity and competition between enzymes in silico. Nat Biotechnol (2004) 1.22

A novel plant cysteine protease has a dual function as a regulator of 1-aminocyclopropane-1-carboxylic Acid synthase gene expression. Plant Cell (2005) 1.21

Detection of Epstein-Barr virus BGLF4 protein kinase in virus replication compartments and virus particles. J Gen Virol (2005) 1.21

Modeling promiscuity based on in vitro safety pharmacology profiling data. ChemMedChem (2007) 1.21

Novel enzyme activities and functional plasticity revealed by recombining highly homologous enzymes. Chem Biol (2001) 1.20

Kynurenine aminotransferase and glutamine transaminase K of Escherichia coli: identity with aspartate aminotransferase. Biochem J (2001) 1.19

Identifying latent enzyme activities: substrate ambiguity within modern bacterial sugar kinases. Biochemistry (2004) 1.17

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When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Proteins (2000) 1.09

Ligand specificity of nuclear hormone receptors: sifting through promiscuity. Biochemistry (2007) 1.09

Diversity and regulation in the NF-kappaB system. Trends Biochem Sci (2007) 1.09

Evolutionary plasticity of protein families: coupling between sequence and structure variation. Proteins (2005) 1.06

Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition. PLoS One (2007) 1.06

Why metabolic enzymes are essential or nonessential for growth of Escherichia coli K12 on glucose. Biochemistry (2007) 1.02

Small heat shock proteins, the cytoskeleton, and inclusion body formation. Neuropathol Appl Neurobiol (2000) 1.00

Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry (2004) 1.00

Sub-cellular localization and post-translational modifications of the Plasmodium yoelii enolase suggest moonlighting functions. Malar J (2007) 1.00

Functional promiscuity correlates with conformational heterogeneity in A-class glutathione S-transferases. J Biol Chem (2007) 0.99

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Ribosomal protein S6 kinase 1 signaling regulates mammalian life span. Science (2009) 7.80

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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

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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

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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

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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

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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

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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

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Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins. Genome Biol (2005) 1.33

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The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics (2002) 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

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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

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Ligand selectivity and competition between enzymes in silico. Nat Biotechnol (2004) 1.22

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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

The structural basis of allosteric regulation in proteins. FEBS Lett (2009) 1.18

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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

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Evolution of enzymes and pathways for the biosynthesis of cofactors. Nat Prod Rep (2007) 1.07

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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

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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

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