Published in Biochemistry on November 09, 2004
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Structure-based insights into the catalytic power and conformational dexterity of peroxiredoxins. Antioxid Redox Signal (2011) 1.79
Substrate specificity and redox potential of AhpC, a bacterial peroxiredoxin. Proc Natl Acad Sci U S A (2007) 1.62
Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Direct (2007) 1.61
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid. Protein Sci (2008) 1.54
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics (2008) 1.41
Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis. Proteins (2010) 1.39
An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput Biol (2009) 1.26
Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J Mol Biol (2009) 1.26
Functional plasticity of a peroxidase allows evolution of diverse disulfide-reducing pathways. Proc Natl Acad Sci U S A (2008) 1.22
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Peroxiredoxins: guardians against oxidative stress and modulators of peroxide signaling. Trends Biochem Sci (2015) 1.14
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A primer on peroxiredoxin biochemistry. Free Radic Biol Med (2014) 1.05
Tuning of peroxiredoxin catalysis for various physiological roles. Biochemistry (2014) 1.02
Kinetic and thermodynamic features reveal that Escherichia coli BCP is an unusually versatile peroxiredoxin. Biochemistry (2011) 1.01
Evolution of function in the "two dinucleotide binding domains" flavoproteins. PLoS Comput Biol (2007) 1.00
Signaling actions of electrophiles: anti-inflammatory therapeutic candidates. Mol Interv (2010) 0.93
Structural and biochemical characterization of peroxiredoxin Qbeta from Xylella fastidiosa: catalytic mechanism and high reactivity. J Biol Chem (2010) 0.90
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Nitration transforms a sensitive peroxiredoxin 2 into a more active and robust peroxidase. J Biol Chem (2014) 0.84
The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers. Protein Sci (2008) 0.84
Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity. Protein Sci (2015) 0.82
Prediction of function in protein superfamilies. F1000 Biol Rep (2009) 0.80
A DNA-binding peroxiredoxin of Coxiella burnetii is involved in countering oxidative stress during exponential-phase growth. J Bacteriol (2010) 0.80
The cysteine-rich protein thimet oligopeptidase as a model of the structural requirements for S-glutathiolation and oxidative oligomerization. PLoS One (2012) 0.79
Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model (2014) 0.79
Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins. Front Pharmacol (2015) 0.78
Distribution and Features of the Six Classes of Peroxiredoxins. Mol Cells (2016) 0.78
Insights into the Function of a Second, Nonclassical Ahp Peroxidase, AhpA, in Oxidative Stress Resistance in Bacillus subtilis. J Bacteriol (2016) 0.77
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput Biol (2017) 0.77
MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs. Genome Biol (2008) 0.77
Sphingosine-1-phosphate in inflammatory bowel disease and colitis-associated colon cancer: the fat's in the fire. Transl Cancer Res (2015) 0.77
Cross-talk between circadian clocks, sleep-wake cycles, and metabolic networks: Dispelling the darkness. Bioessays (2016) 0.76
ATP and Mg2+ promote the reversible oligomerization and aggregation of chloroplast 2-Cys peroxiredoxin. J Biol Chem (2011) 0.75
Insights into Trx1, TRP14, and Prx1 homologs of Paralichthys olivaceus: molecular profiles and transcriptional responses to immune stimulations. Fish Physiol Biochem (2015) 0.75
An effective method for profiling the selenium-binding proteins using its reactive metabolic intermediate. J Biol Inorg Chem (2015) 0.75
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res (2003) 4.83
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol (2009) 4.76
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res (2006) 3.40
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One (2009) 3.03
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry (2006) 2.65
Evolution of enzyme superfamilies. Curr Opin Chem Biol (2006) 2.30
Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol (2007) 2.29
Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys (2005) 2.18
Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure (2008) 1.91
The Enzyme Function Initiative. Biochemistry (2011) 1.87
Automated discovery of 3D motifs for protein function annotation. Bioinformatics (2006) 1.60
A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol (2006) 1.52
The Structure-Function Linkage Database. Nucleic Acids Res (2013) 1.50
Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature (2013) 1.46
Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem (2011) 1.40
Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry (2003) 1.36
Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol (2009) 1.36
Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol (2006) 1.31
Glutathione transferases are structural and functional outliers in the thioredoxin fold. Biochemistry (2009) 1.30
An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput Biol (2009) 1.26
Differential use of protease families for invasion by schistosome cercariae. Biochimie (2007) 1.24
Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci (2009) 1.23
At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate. Biochemistry (2008) 1.22
Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature (2013) 1.22
Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput (2005) 1.19
Inference of functional properties from large-scale analysis of enzyme superfamilies. J Biol Chem (2011) 1.17
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A (2012) 1.17
Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Comput Biol (2013) 1.17
Pythoscape: a framework for generation of large protein similarity networks. Bioinformatics (2012) 1.15
Superfamily active site templates. Proteins (2004) 1.15
structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics (2007) 1.14
Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry (2008) 1.12
Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans. Biochemistry (2007) 1.10
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics (2010) 1.09
The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg(2+)-NO(3)(-)-creatine transition-state analogue complex. Biochemistry (2002) 1.09
A mapping of drug space from the viewpoint of small molecule metabolism. PLoS Comput Biol (2009) 1.09
Toward mechanistic classification of enzyme functions. Curr Opin Chem Biol (2011) 1.08
Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc Natl Acad Sci U S A (2013) 1.06
Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes. Biochemistry (2009) 1.04
The global cysteine peptidase landscape in parasites. Trends Parasitol (2009) 1.02
D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily. Biochemistry (2006) 1.02
The Structure Superposition Database. Nucleic Acids Res (2003) 1.01
Evolution of function in the "two dinucleotide binding domains" flavoproteins. PLoS Comput Biol (2007) 1.00
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics (2009) 1.00
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol (2010) 1.00
Mechanisms of protein evolution and their application to protein engineering. Adv Enzymol Relat Areas Mol Biol (2007) 0.98
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol (2008) 0.98
Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways. Chem Biol (2008) 0.97
Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry (2007) 0.96
Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry (2002) 0.96
Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One (2007) 0.95
The evolution of function in strictosidine synthase-like proteins. Proteins (2011) 0.92
Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase. Biochemistry (2007) 0.92
Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A (2013) 0.91
SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis (2009) 0.89
Evidence of the participation of remote residues in the catalytic activity of Co-type nitrile hydratase from Pseudomonas putida. Biochemistry (2011) 0.87
Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily. Biochemistry (2009) 0.87
Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies. Curr Opin Struct Biol (2011) 0.86
[FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. Biochemistry (2015) 0.86
Comparison of methods for genomic localization of gene trap sequences. BMC Genomics (2006) 0.84
A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes. AAPS PharmSci (2003) 0.82
Expression of Torpedo californica creatine kinase in Escherichia coli and purification from inclusion bodies. Protein Expr Purif (2002) 0.80
Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase. Biochemistry (2004) 0.80
A bulky hydrophobic residue is not required to maintain the V-conformation of enzyme-bound thiamin diphosphate. Biochemistry (2013) 0.79
Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model (2014) 0.79
Mechanistic and bioinformatic investigation of a conserved active site helix in α-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. Biochemistry (2014) 0.76
Cloning, expression, purification and characterization of an iron-dependent regulator protein from Thermobifida fusca. Protein Expr Purif (2013) 0.76
A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. PLoS Negl Trop Dis (2012) 0.75
Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633. J Bacteriol (2003) 0.75
Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry (2015) 0.75
Time-of-flight neutron diffraction study of bovine γ-chymotrypsin at the Protein Crystallography Station. Acta Crystallogr Sect F Struct Biol Cryst Commun (2011) 0.75
Changes to NIH grant system may backfire. Science (2008) 0.75
Intersect: identification and visualization of overlaps in database search results. Bioinformatics (2003) 0.75