PubRank

Barry L Stoddard

Author PubWeight™ 137.18‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Design of a novel globular protein fold with atomic-level accuracy. Science 2003 13.06
2 De novo computational design of retro-aldol enzymes. Science 2008 7.62
3 A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 2003 7.56
4 Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 2010 4.32
5 Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 2006 4.06
6 The crystal structure of TAL effector PthXo1 bound to its DNA target. Science 2012 3.69
7 Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol 2004 3.66
8 Computational thermostabilization of an enzyme. Science 2005 2.79
9 Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase. Structure 2002 2.56
10 Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell 2002 2.25
11 Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Genes Dev 2003 2.23
12 Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat Biotechnol 2012 2.19
13 Accumulation of free ADP-ribose from mitochondria mediates oxidative stress-induced gating of TRPM2 cation channels. J Biol Chem 2004 2.08
14 The tertiary structure and domain organization of coagulation factor VIII. Blood 2007 1.96
15 Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol 2006 1.93
16 Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J Mol Biol 2003 1.93
17 DNA binding and cleavage by the HNH homing endonuclease I-HmuI. J Mol Biol 2004 1.86
18 The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure 2006 1.81
19 The structure of Escherichia coli cytosine deaminase. J Mol Biol 2002 1.81
20 Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease. Proc Natl Acad Sci U S A 2009 1.79
21 Exploitation of binding energy for catalysis and design. Nature 2009 1.77
22 Homing endonuclease I-CreI derivatives with novel DNA target specificities. Nucleic Acids Res 2006 1.75
23 Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity. Nucleic Acids Res 2010 1.66
24 Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure 2008 1.64
25 Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res 2010 1.58
26 Alteration of enzyme specificity by computational loop remodeling and design. Proc Natl Acad Sci U S A 2009 1.56
27 Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat Chem Biol 2012 1.50
28 Coevolution of a homing endonuclease and its host target sequence. J Mol Biol 2007 1.49
29 Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation. Nucleic Acids Res 2008 1.44
30 Isolation and characterization of new homing endonuclease specificities at individual target site positions. J Mol Biol 2004 1.44
31 High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display. Nucleic Acids Res 2009 1.43
32 Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci U S A 2011 1.39
33 Catalytic mechanisms of restriction and homing endonucleases. Biochemistry 2002 1.34
34 Single-strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV vector template. Nucleic Acids Res 2010 1.32
35 megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. Nucleic Acids Res 2013 1.30
36 The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy. Structure 2003 1.26
37 TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol 2013 1.24
38 Microseed matrix screening to improve crystals of yeast cytosine deaminase. Acta Crystallogr D Biol Crystallogr 2004 1.22
39 Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family. Nucleic Acids Res 2011 1.21
40 Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry 2004 1.18
41 Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase. Nucleic Acids Res 2004 1.18
42 NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase. J Biol Chem 2002 1.15
43 The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. EMBO J 2007 1.15
44 Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy. Protein Eng Des Sel 2004 1.14
45 Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins. Nucleic Acids Res 2009 1.14
46 Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI. Structure 2010 1.11
47 Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI. Structure 2010 1.10
48 Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I. J Mol Biol 2008 1.10
49 The crystal structure and mutational analysis of human NUDT9. J Mol Biol 2003 1.07
50 Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases. Nucleic Acids Res 2007 1.07
51 Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family. Nucleic Acids Res 2009 1.05
52 Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI. Nucleic Acids Res 2011 1.03
53 Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Nucleic Acids Res 2012 1.02
54 Thermodynamics of DNA target site recognition by homing endonucleases. Nucleic Acids Res 2007 1.01
55 TAL effectors: function, structure, engineering and applications. Curr Opin Struct Biol 2012 0.99
56 Alanine-scanning mutagenesis reveals a cytosine deaminase mutant with altered substrate preference. Biochemistry 2004 0.98
57 I-BasI and I-HmuI: two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities. J Mol Biol 2006 0.96
58 Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism. Biochemistry 2007 0.95
59 Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases. Nucleic Acids Res 2008 0.94
60 Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. J Am Chem Soc 2013 0.93
61 Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. J Mol Biol 2006 0.93
62 Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo. Cancer Res 2009 0.92
63 The design and in vivo evaluation of engineered I-OnuI-based enzymes for HEG gene drive. PLoS One 2013 0.91
64 The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease. Structure 2009 0.91
65 Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine. J Mol Biol 2008 0.91
66 Surface-exposed hemophilic mutations across the factor VIII C2 domain have variable effects on stability and binding activities. J Biol Chem 2004 0.90
67 PARP-mediated repair, homologous recombination, and back-up non-homologous end joining-like repair of single-strand nicks. DNA Repair (Amst) 2013 0.90
68 Disruption of protein-membrane binding and identification of small-molecule inhibitors of coagulation factor VIII. Chem Biol 2004 0.89
69 LAHEDES: the LAGLIDADG homing endonuclease database and engineering server. Nucleic Acids Res 2012 0.87
70 DNA recognition and transcriptional regulation by the WhiA sporulation factor. Sci Rep 2011 0.87
71 Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms. Nucleic Acids Res 2012 0.86
72 Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space. Nucleic Acids Res 2012 0.86
73 Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization. Proc Natl Acad Sci U S A 2014 0.86
74 Homology modeling and mutational analysis of Ho endonuclease of yeast. Genetics 2004 0.84
75 Optimization of factor VIII replacement therapy: can structural studies help in evading antibody inhibitors? Br J Haematol 2002 0.81
76 Rapid determination of homing endonuclease DNA binding specificity profile. Methods Mol Biol 2014 0.80
77 Breakthrough articles: putting science first. Nucleic Acids Res 2014 0.77
78 Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization. Methods Mol Biol 2015 0.77
79 Corrigendum: Biocontainment of genetically modified organisms by synthetic protein design. Nature 2015 0.76
80 Nuclease enzymes. Methods 2002 0.75
81 Editorial: Alfred Pingoud (1945-2015). Nucleic Acids Res 2015 0.75