List of works - Barry L Stoddard

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

scientific article

Accumulation of free ADP-ribose from mitochondria mediates oxidative stress-induced gating of TRPM2 cation channels

scientific article

Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I.

scientific article published on 12 November 2008

Alteration of enzyme specificity by computational loop remodeling and design

scientific article

Bacterial Cytosine Deaminase Mutants Created by Molecular Engineering Show Improved 5-Fluorocytosine-Mediated Cell Killing In vitro and In vivo

scientific article

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

scientific article

Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy

scientific article

Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface

scientific article

Computational design of ligand-binding proteins with high affinity and selectivity

scientific article

Computational protein design enables a novel one-carbon assimilation pathway.

scientific article

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

scientific article

Computational redesign of endonuclease DNA binding and cleavage specificity

scientific article

Computational redesign of protein-protein interaction specificity

scientific article

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

scientific article

Computational thermostabilization of an enzyme

scientific article published on May 2005

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

scientific article

Control of repeat-protein curvature by computational protein design

scientific article

DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target

scientific article

De novo computational design of retro-aldol enzymes

scientific article

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

scientific article

Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces

scientific article published in 2021

Design, activity, and structure of a highly specific artificial endonuclease

scientific article

Efficient Modification of the CCR5 Locus in Primary Human T Cells With megaTAL Nuclease Establishes HIV-1 Resistance

scientific article published on 23 August 2016

Engineering and functionalization of large circular tandem repeat protein nanoparticles

scientific article published on 23 March 2020

Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases

scientific article

Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization

scientific article published on January 2015

Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space

scientific article

Exploitation of binding energy for catalysis and design

scientific article published on October 2009

Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases

scientific article

Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI ⬇️

scientific article published on August 26, 2010

Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease

scholarly article

Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins

scientific article

High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display

scientific article published on 08 September 2009

Homing endonuclease I-CreI derivatives with novel DNA target specificities

scientific article

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

scientific article

Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity

scientific article published on 27 April 2016

Isolation and characterization of new homing endonuclease specificities at individual target site positions

scientific article

LAHEDES: the LAGLIDADG homing endonuclease database and engineering server

scientific article

Microseed matrix screening to improve crystals of yeast cytosine deaminase

scientific article published on 25 February 2004

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution

scientific article published on 4 August 2006

NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase.

scientific article

Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition

scientific article published on 27 April 2020

Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation

scientific article

Precise assembly of complex beta sheet topologies from de novo designed building blocks

scientific article published on 9 December 2015

Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy

scientific article published in August 2004

Rational design of α-helical tandem repeat proteins with closed architectures

scientific article

Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase

scientific article

Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases

scientific article

Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization

scientific article published on 03 March 2014

Structural Analyses of Covalent Enzyme–Substrate Analog Complexes Reveal Strengths and Limitations of De Novo Enzyme Design

scientific article

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor

scientific article

Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI

scientific article published on 01 January 2019

Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding

scientific article

Surface-exposed hemophilic mutations across the factor VIII C2 domain have variable effects on stability and binding activities

scientific article

Tapping natural reservoirs of homing endonucleases for targeted gene modification

scientific article

The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy

scientific article

The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease

scientific article published on 15 December 2015

The Structure of a Bacterial DUF199/WhiA Protein: Domestication of an Invasive Endonuclease

scientific article

The crystal structure and mutational analysis of human NUDT9

scientific article

The design and in vivo evaluation of engineered I-OnuI-based enzymes for HEG gene drive ⬇️

scientific article

The structure of Escherichia coli cytosine deaminase

scientific article

The tertiary structure and domain organization of coagulation factor VIII

scientific article

Thermodynamics of DNA target site recognition by homing endonucleases.

scientific article published on 18 October 2007

Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses

scientific article published on July 2017

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

scientific article published on 01 October 2018

Unusual Target Site Disruption by the Rare-Cutting HNH Restriction Endonuclease PacI

scientific article

Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine

scientific article published on 11 January 2008

megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering

scientific article

List of works by Barry L Stoddard

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

Accumulation of free ADP-ribose from mitochondria mediates oxidative stress-induced gating of TRPM2 cation channels

Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I.

Alteration of enzyme specificity by computational loop remodeling and design

Bacterial Cytosine Deaminase Mutants Created by Molecular Engineering Show Improved 5-Fluorocytosine-Mediated Cell Killing In vitro and In vivo

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy

Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface

Computational design of ligand-binding proteins with high affinity and selectivity

Computational protein design enables a novel one-carbon assimilation pathway.

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

Computational redesign of endonuclease DNA binding and cleavage specificity

Computational redesign of protein-protein interaction specificity

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

Computational thermostabilization of an enzyme

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

Control of repeat-protein curvature by computational protein design

DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target

De novo computational design of retro-aldol enzymes

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces

Design, activity, and structure of a highly specific artificial endonuclease

Efficient Modification of the CCR5 Locus in Primary Human T Cells With megaTAL Nuclease Establishes HIV-1 Resistance

Engineering and functionalization of large circular tandem repeat protein nanoparticles

Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases

Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization

Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space

Exploitation of binding energy for catalysis and design

Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases

Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI ⬇️

Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease

Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins

High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display

Homing endonuclease I-CreI derivatives with novel DNA target specificities

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity

Isolation and characterization of new homing endonuclease specificities at individual target site positions

LAHEDES: the LAGLIDADG homing endonuclease database and engineering server

Microseed matrix screening to improve crystals of yeast cytosine deaminase

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution

NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase.

Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition

Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation

Precise assembly of complex beta sheet topologies from de novo designed building blocks

Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy

Rational design of α-helical tandem repeat proteins with closed architectures

Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase

Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases

Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization

Structural Analyses of Covalent Enzyme–Substrate Analog Complexes Reveal Strengths and Limitations of De Novo Enzyme Design

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor

Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI

Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding

Surface-exposed hemophilic mutations across the factor VIII C2 domain have variable effects on stability and binding activities

Tapping natural reservoirs of homing endonucleases for targeted gene modification

The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy

The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease

The Structure of a Bacterial DUF199/WhiA Protein: Domestication of an Invasive Endonuclease

The crystal structure and mutational analysis of human NUDT9

The design and in vivo evaluation of engineered I-OnuI-based enzymes for HEG gene drive ⬇️

The structure of Escherichia coli cytosine deaminase

The tertiary structure and domain organization of coagulation factor VIII

Thermodynamics of DNA target site recognition by homing endonucleases.

Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

Unusual Target Site Disruption by the Rare-Cutting HNH Restriction Endonuclease PacI

Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine

megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering