Published in PLoS One on February 16, 2012
Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution. Angew Chem Int Ed Engl (2015) 1.05
Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys (2013) 0.89
An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues. PLoS One (2012) 0.83
A computational module assembled from different protease family motifs identifies PI PLC from Bacillus cereus as a putative prolyl peptidase with a serine protease scaffold. PLoS One (2013) 0.80
A measure of the broad substrate specificity of enzymes based on 'duplicate' catalytic residues. PLoS One (2012) 0.79
Enumerating pathways of proton abstraction based on a spatial and electrostatic analysis of residues in the catalytic site. PLoS One (2012) 0.78
Molecular annotation of ketol-acid reductoisomerases from Streptomyces reveals a novel amino acid biosynthesis interlock mediated by enzyme promiscuity. Microb Biotechnol (2014) 0.77
Biological messiness vs. biological genius: Mechanistic aspects and roles of protein promiscuity. J Steroid Biochem Mol Biol (2014) 0.76
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. PLoS Comput Biol (2016) 0.75
Facilitating the Evolution of Esterase Activity from a Promiscuous Enzyme (Mhg) with Catalytic Functions of Amide Hydrolysis and Carboxylic Acid Perhydrolysis by Engineering the Substrate Entrance Tunnel. Appl Environ Microbiol (2016) 0.75
MEPPitope: spatial, electrostatic and secondary structure perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus. F1000Res (2016) 0.75
Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template. F1000Res (2014) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A (2001) 42.14
Classical electrostatics in biology and chemistry. Science (1995) 17.26
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res (2004) 11.53
Pseudoallelism and gene evolution. Cold Spring Harb Symp Quant Biol (1951) 10.02
Evolution and tinkering. Science (1977) 9.07
Kemp elimination catalysts by computational enzyme design. Nature (2008) 8.19
De novo protein design: fully automated sequence selection. Science (1997) 7.86
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res (2004) 7.21
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
The 'evolvability' of promiscuous protein functions. Nat Genet (2004) 5.41
Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem (2010) 4.41
Structure-based activity prediction for an enzyme of unknown function. Nature (2007) 3.65
Catalytic promiscuity and the evolution of new enzymatic activities. Chem Biol (1999) 3.54
Enzyme-like proteins by computational design. Proc Natl Acad Sci U S A (2001) 3.43
New algorithms and an in silico benchmark for computational enzyme design. Protein Sci (2006) 3.40
The Kyoto encyclopedia of genes and genomes--KEGG. Yeast (2000) 3.27
Retracted Computational design of a biologically active enzyme. Science (2004) 3.25
Conformational diversity and protein evolution--a 60-year-old hypothesis revisited. Trends Biochem Sci (2003) 3.24
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A (2007) 3.15
Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol (2009) 3.13
Designed divergent evolution of enzyme function. Nature (2006) 3.09
Recognition of spatial motifs in protein structures. J Mol Biol (1999) 2.94
Protein promiscuity and its implications for biotechnology. Nat Biotechnol (2009) 2.78
In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A (2009) 2.66
Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol (2003) 2.56
The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry (2011) 2.42
How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41
Evolution of enzyme superfamilies. Curr Opin Chem Biol (2006) 2.30
Evolving strategies for enzyme engineering. Curr Opin Struct Biol (2005) 2.20
Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys (2005) 2.18
Protein design by directed evolution. Annu Rev Biophys (2008) 2.15
Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol (1998) 2.15
Moonlighting proteins--an update. Mol Biosyst (2009) 2.08
Triosephosphate isomerase catalysis is diffusion controlled. Appendix: Analysis of triose phosphate equilibria in aqueous solution by 31P NMR. Biochemistry (1988) 1.97
Thermodynamics of neutral protein evolution. Genetics (2006) 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
Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J (2007) 1.75
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics (2010) 1.72
Protein folds and functions. Structure (1998) 1.69
Enzyme promiscuity: mechanism and applications. Trends Biotechnol (2007) 1.65
Messy biology and the origins of evolutionary innovations. Nat Chem Biol (2010) 1.61
Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways. Angew Chem Int Ed Engl (2004) 1.47
Structural plasticity broadens the specificity of an engineered protease. Nature (1989) 1.44
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics (2008) 1.41
Protein engineers turned evolutionists. Nat Methods (2007) 1.35
DNA and the neutral theory. Philos Trans R Soc Lond B Biol Sci (1986) 1.27
What makes an enzyme promiscuous? Curr Opin Chem Biol (2010) 1.17
A structural model of latent evolutionary potentials underlying neutral networks in proteins. HFSP J (2007) 1.15
Domain mobility in proteins: functional and evolutionary implications. Brief Bioinform (2009) 1.11
A quantitative index of substrate promiscuity. Biochemistry (2007) 1.09
FLORA: a novel method to predict protein function from structure in diverse superfamilies. PLoS Comput Biol (2009) 1.09
An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily. Proc Natl Acad Sci U S A (2010) 1.07
Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry (2007) 0.96
Catalysis by ribonuclease A is limited by the rate of substrate association. Biochemistry (2003) 0.94
Natural distribution. Math Biosci (2007) 0.93
Electrostatics in the active site of an alpha-amylase. Eur J Biochem (1999) 0.93
Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase. PLoS One (2011) 0.90
The subtle benefits of being promiscuous: adaptive evolution potentiated by enzyme promiscuity. HFSP J (2007) 0.90
Early evolution of the biotin-dependent carboxylase family. BMC Evol Biol (2011) 0.87
Enzyme catalytic promiscuity: the nonheme Fe2+ center of beta-diketone-cleaving dioxygenase Dke1 promotes hydrolysis of activated esters. Chembiochem (2010) 0.84
Protein promiscuity: drug resistance and native functions--HIV-1 case. J Biomol Struct Dyn (2005) 0.82
Prediction of function in protein superfamilies. F1000 Biol Rep (2009) 0.80
Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures. Mol Biosyst (2010) 0.79
Engineering heme binding sites in monomeric rop. J Biol Inorg Chem (2009) 0.76
Translin binding to DNA: recruitment through DNA ends and consequent conformational transitions. Biochemistry (2002) 0.93
A homologue of the defender against the apoptotic death gene (dad1 )in UV-exposed Chlamydomonas cells is downregulated with the onset of programmed cell death. J Biosci (2007) 0.92
Expression pattern of Drosophila translin and behavioral analyses of the mutant. Eur J Cell Biol (2007) 0.92
Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase. PLoS One (2011) 0.90
Crystal structures of Drosophila mutant translin and characterization of translin variants reveal the structural plasticity of translin proteins. FEBS J (2008) 0.90
Chromosome territories reposition during DNA damage-repair response. Genome Biol (2013) 0.89
Co-expressed recombinant human Translin-Trax complex binds DNA. FEBS Lett (2005) 0.89
Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences. J Theor Biol (2006) 0.89
Homologous recombination properties of OsRad51, a recombinase from rice. Plant Mol Biol (2008) 0.85
Mitochondrial tRNA sequences as unusual replication origins: pathogenic implications for Homo sapiens. J Theor Biol (2006) 0.84
ATP hydrolysis induces expansion of MutS contacts on heteroduplex: a case for MutS treadmilling? Biochemistry (2002) 0.84
UVI31+ is a DNA endonuclease that dynamically localizes to chloroplast pyrenoids in C. reinhardtii. PLoS One (2012) 0.84
Inhibition of a cold-active alkaline phosphatase by imipenem revealed by in silico modeling of metallo-β-lactamase active sites. FEBS Lett (2012) 0.84
DNA mediated disassembly of hRad51 and hRad52 proteins and recruitment of hRad51 to ssDNA by hRad52. FEBS J (2006) 0.83
Low energy electron induced damage to plasmid DNA pQE30. J Chem Phys (2012) 0.82
Interaction of hRad51 and hRad52 with MCM complex: a cross-talk between recombination and replication proteins. Biochem Biophys Res Commun (2005) 0.82
Human Rad52 facilitates a three-stranded pairing that follows no strand exchange: a novel pairing function of the protein. Biochemistry (2003) 0.82
Enhanced DNA dynamics due to cationic reagents, topological states of dsDNA and high mobility group box 1 as probed by PicoGreen. FEBS J (2008) 0.81
Flagella-generated forces reveal gear-type motor in single cells of the green alga, Chlamydomonas reinhardtii. Biochem Biophys Res Commun (2009) 0.81
DNA dynamics in RecA-DNA filaments: ATP hydrolysis-related flexibility in DNA. Biochemistry (2003) 0.81
DNA strand exchange activity of rice recombinase OsDmc1 monitored by fluorescence resonance energy transfer and the role of ATP hydrolysis. FEBS J (2006) 0.81
A computational module assembled from different protease family motifs identifies PI PLC from Bacillus cereus as a putative prolyl peptidase with a serine protease scaffold. PLoS One (2013) 0.80
p53 suppresses BRCA2-stimulated ATPase and strand exchange functions of human RAD51. J Biochem (2013) 0.80
Fluorescence characterization of the structural heterogeneity of polytene chromosomes. J Fluoresc (2009) 0.80
Human Rad51 mediated DNA unwinding is facilitated by conditions that favour Rad51-dsDNA aggregation. BMC Biochem (2009) 0.79
A measure of the broad substrate specificity of enzymes based on 'duplicate' catalytic residues. PLoS One (2012) 0.79
Fluorescence dynamics of double- and single-stranded DNA bound to histone and micellar surfaces. J Phys Chem B (2010) 0.79
Relationship between mRNA secondary structure and sequence variability in Chloroplast genes: possible life history implications. BMC Genomics (2008) 0.78
A comparative approach to elucidate chloroplast genome replication. BMC Genomics (2009) 0.78
GTP-induced conformational changes in translin: a comparison between human and Drosophila proteins. Biochemistry (2006) 0.78
Promiscuity-based enzyme selection for rational directed evolution experiments. Methods Mol Biol (2013) 0.78
IMACULAT - an open access package for the quantitative analysis of chromosome localization in the nucleus. PLoS One (2013) 0.78
RecA-promoted sliding of base pairs within DNA repeats: quantitative analysis by a slippage assay. Biochem Biophys Res Commun (2002) 0.77
Regulation of CCM genes in Chlamydomonas reinhardtii during conditions of light-dark cycles in synchronous cultures. Plant Mol Biol (2014) 0.77
A single mismatch in the DNA induces enhanced aggregation of MutS. Hydrodynamic analyses of the protein-DNA complexes. FEBS J (2005) 0.77
A novel approach for uniform (13)C and (15)N labeling of DNA for NMR studies. Biochem Biophys Res Commun (2002) 0.76
Effect of DNA sequence and nucleotide cofactors on hRad51 binding to ssDNA: role of hRad52 in recruitment. Biochem Biophys Res Commun (2005) 0.76
¹H, ¹³C and ¹⁵N resonance assignments of S114A mutant of UVI31+ from Chlamydomonas reinhardtii. Biomol NMR Assign (2012) 0.75
Overexpression and purification of isotopically labeled Escherichia coli MutH for NMR studies. Protein Expr Purif (2003) 0.75
Flagella as a novel alignment medium for the measurement of residual dipolar couplings in proteins. Chem Commun (Camb) (2013) 0.75
Corrigendum: The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines. Sci Rep (2016) 0.75
MutS and UvrD proteins stimulate exonuclease action: insights into exonuclease-mediated strand repair. Biochemistry (2009) 0.75
Klenow exo-, as opposed to exo+, traverses through G-G:C triplex by melting G-G base pairs. Biochem Biophys Res Commun (2002) 0.75