List of works - Patricia Babbitt

3-Carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida is homologous to the class II fumarase family: a new reaction in the evolution of a mechanistic motif

scientific article published on October 13, 1992

A Global Comparison of the Human and T. brucei Degradomes Gives Insights about Possible Parasite Drug Targets ⬇️

scientific article published on December 6, 2012

A comparative study of human muscle and brain creatine kinases expressed in Escherichia coli

scientific article published on January 2000

A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids

scientific article published on February 1995

A global view of structure-function relationships in the tautomerase superfamily.

scientific article published on 28 November 2017

A gold standard set of mechanistically diverse enzyme superfamilies

scientific article

A large-scale evaluation of computational protein function prediction

scientific article

A mapping of drug space from the viewpoint of small molecule metabolism

scientific article

A novel activity of OmpT. Proteolysis under extreme denaturing conditions.

scientific article published in June 1995

A novel structural basis for membrane association of a protein: construction of a chimeric soluble mutant of (S)-mandelate dehydrogenase from Pseudomonas putida

scientific article published on December 1993

A semiautomated approach to gene discovery through expressed sequence tag data mining: Discovery of new human transporter genes ⬇️

scientific article published on January 1, 2003

A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function

scientific article published on 01 January 2020

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

scientific article

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences

scientific article published on 5 January 2017

An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations

scientific article published on 23 October 2009

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases

scientific article published on June 23, 1992

Annotating Enzymes of Uncertain Function: The Deacylation of d -Amino Acids by Members of the Amidohydrolase Superfamily ,

scientific article

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

scientific article

At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate

scientific article published on 3 January 2008

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug and Play” Domain

scientific article published on 24 July 2018

Automated discovery of 3D motifs for protein function annotation

scientific article published on 12 January 2006

Barrels in pieces?

scientific article published on 01 January 2001

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells

scientific article published on January 2003

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space

scientific article

Biocuration in the structure-function linkage database: the anatomy of a superfamily

scientific article

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

scientific article

Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric-8.

scientific article published on June 2009

Can sequence determine function?

scientific article

Changes to NIH Grant System May Backfire

scientific article

Cloning and expression of functional rabbit muscle creatine kinase in Escherichia coli. Addressing the problem of microheterogeneity

scientific article published in June 1991

Cloning and functional characterization of a rat renal organic cation transporter isoform (rOCT1A).

scientific article published on June 1997

Comparison of methods for genomic localization of gene trap sequences

scientific article published on 18 September 2006

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

scientific article

Consequences of domain insertion on sequence-structure divergence in a superfold

scientific article published on 19 August 2013

Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis

scientific article

Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases

scientific journal article

Creatine kinase protein sequence encoded by a cDNA made from Torpedo californica electric organ mRNA.

scientific article

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

scientific article

D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily

scientific article

DASP3: identification of protein sequences belonging to functionally relevant groups

scientific article

Definitions of enzyme function for the structural genomics era.

scientific article

Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification

scientific article published on 8 April 2015

Differential use of protease families for invasion by schistosome cercariae

scientific article

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening

scientific article

Discovery of new enzymes and metabolic pathways by using structure and genome context

scientific article

Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor

scientific article published on November 2004

Divergent evolution in enolase superfamily: strategies for assigning functions

scientific article

Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity

scientific article

Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies

scientific article (publication date: 2001)

Effusion: prediction of protein function from sequence similarity networks

scientific article published on 01 February 2019

Enzyme (re)design: lessons from natural evolution and computation

scientific article published on 23 February 2009

Evaluating Functional Annotations of Enzymes Using the Gene Ontology

scientific article published on January 2017

Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723.

scientific article published in June 1999

Evolution of Enzymatic Activities in the Enolase Superfamily: Characterization of the (D)-Glucarate/Galactarate Catabolic Pathway in Escherichia coli ⬇️

scientific article published on October 13, 1998

Evolution of Enzymatic Activities in the Enolase Superfamily: Crystal Structure of (D)-Glucarate Dehydratase from Pseudomonas putida, ⬇️

scientific article published on October 13, 1998

Evolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms in Two Families of cis , cis -Muconate Lactonizing Enzymes † ‡

scientific article

Evolution of Enzymatic Activities in the Enolase Superfamily: l -Rhamnonate Dehydratase † ‡

scientific article

Evolution of an enzyme active site: The structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase ⬇️

scientific article published on September 1, 1998

Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans

scientific article

Evolution of enzyme superfamilies

scientific article published on 28 August 2006

Evolution of function in the "two dinucleotide binding domains" flavoproteins

scientific article

Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily

scientific article published on 11 May 2006

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies

scientific article

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily

scientific article

Evolutionary constraints on structural similarity in orthologs and paralogs

scientific article published on June 2009

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

scientific article

Evolutionary reprograming of protein-protein interaction specificity

scientific article published on 22 October 2015

Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily

scientific article published in November 1996

Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions

scientific article published on 17 April 2019

Expression of Torpedo californica creatine kinase in Escherichia coli and purification from inclusion bodies

scientific article published in October 2002

Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches.

scientific article

Glutathione transferases are structural and functional outliers in the thioredoxin fold

scientific article

Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase

scientific article

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

scientific article

Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.

scientific article

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution

scientific article

Inference of Functional Properties from Large-scale Analysis of Enzyme Superfamilies ⬇️

scientific article published on November 8, 2011

Insights into the Mechanism of Catalysis by the P−C Bond-Cleaving Enzyme Phosphonoacetaldehyde Hydrolase Derived from Gene Sequence Analysis and Mutagenesis ⬇️

scientific article published on June 30, 1998

Integrated tools for structural and sequence alignment and analysis

scientific article published on January 2000

InterPro in 2017-beyond protein family and domain annotations

scientific article

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

article by Alex Mitchell et al published 6 November 2018 in Nucleic Acids Research

Intersect: identification and visualization of overlaps in database search results

scientific article published in October 2003

Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure

scientific article published in January 2005

Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase

scientific article published in November 2004

Key challenges for the creation and maintenance of specialist protein resources

scientific article

Kinetic and structural characterization of a cis-3-Chloroacrylic acid dehalogenase homologue in Pseudomonas sp. UW4: A potential step between subgroups in the tautomerase superfamily

scientific article published on 27 October 2017

Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere

scientific article

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database

scientific article

Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli

scientific article

Mechanisms of protein evolution and their application to protein engineering

scientific article published on January 2007

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

scientific article published on 22 April 2014

Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis

scientific article published on 01 October 1998

Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells

scientific article

Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha

scientific article

Mutagenesis of two acidic active site residues in human muscle creatine kinase: implications for the catalytic mechanism

scientific article published in March 2001

Mutations in PNKD causing paroxysmal dyskinesia alters protein cleavage and stability ⬇️

scientific article (publication date: 15 June 2011)

New computational approaches to understanding molecular protein function

scientific article published on 5 April 2018

New functions from old scaffolds: how nature reengineers enzymes for new functions

scientific article

New insights about enzyme evolution from large scale studies of sequence and structure relationships

scientific article

Novel Enzymic Hydrolytic Dehalogenation of a Chlorinated Aromatic ⬇️

scientific article published on July 12, 1991

On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway

scientific article

Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach

scientific article

Prediction and assignment of function for a divergent N-succinyl amino acid racemase

scientific article

Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

scientific journal article

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily

scientific article

Prediction of substrates for glutathione transferases by covalent docking

scientific article

Pythoscape: a framework for generation of large protein similarity networks ⬇️

scientific article published on September 8, 2012

Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function

scientific article

Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways

scientific article

Reengineering the glutathione S-transferase scaffold: a rational design strategy pays off.

scientific article

Removal of a proteolytic activity associated with aggregates formed from expression of creatine kinase in Escherichia coli leads to improved recovery of active enzyme

scientific article published on October 1, 1990

Representing structure-function relationships in mechanistically diverse enzyme superfamilies.

scientific article published in January 2005

Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks

scientific article published on 27 July 2018

Sequence verification of human creatine kinase (43 kDa) isozymes by high-resolution tandem mass spectrometry

scientific article

Sequence verification of human creatine kinase (43 kDa) isozymes by high-resolution tandem mass spectrometry

scholarly article

Shotgun: getting more from sequence similarity searches

scientific article published on September 1999

SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni

scientific article

Stability for function trade-offs in the enolase superfamily "catalytic module"

scientific article

Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer

scientific article published on 13 April 2020

Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase

scientific article

Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer

scientific article published on 23 May 2019

Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function

scientific article

Superfamily active site templates.

scientific article published in June 2004

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

scientific article published on 14 February 2009

The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg(2+)-NO(3)(-)-creatine transition-state analogue complex

scientific article

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

scientific article published on 19 November 2019

The Enzyme Function Initiative

scientific article

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse

scientific article

The Nucleophilic Attack Six-Bladed β-Propeller (N6P) Superfamily

The Structure Superposition Database

scientific article published on January 2003

The Structure-Function Linkage Database

scientific article

The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids

scientific article published in December 1996

The evolution of function in strictosidine synthase-like proteins

scientific article published on 21 September 2011

The global cysteine peptidase landscape in parasites

scientific article published on 24 October 2009

The principal islet of the Coho salmon (Oncorhyncus kisutch) contains the BB isoenzyme of creatine kinase

scientific article published on October 1, 1992

Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies ⬇️

scientific article published on April 1, 2011

Toward mechanistic classification of enzyme functions

scientific article published on 12 April 2011

Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities

scientific article published on December 1997

Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase

scientific article

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

scientific article

Using the Structure-function Linkage Database to characterize functional domains in enzymes

scientific article published on 01 March 2006

Using the structure-function linkage database to characterize functional domains in enzymes

scientific article

ViewFeature: integrated feature analysis and visualization.

scientific article

[FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis

scientific article published on 2 March 2015

structureViz: linking Cytoscape and UCSF Chimera.

scientific article

List of works by Patricia Babbitt

3-Carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida is homologous to the class II fumarase family: a new reaction in the evolution of a mechanistic motif

A Global Comparison of the Human and T. brucei Degradomes Gives Insights about Possible Parasite Drug Targets ⬇️

A comparative study of human muscle and brain creatine kinases expressed in Escherichia coli

A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids

A global view of structure-function relationships in the tautomerase superfamily.

A gold standard set of mechanistically diverse enzyme superfamilies

A large-scale evaluation of computational protein function prediction

A mapping of drug space from the viewpoint of small molecule metabolism

A novel activity of OmpT. Proteolysis under extreme denaturing conditions.

A novel structural basis for membrane association of a protein: construction of a chimeric soluble mutant of (S)-mandelate dehydrogenase from Pseudomonas putida

A semiautomated approach to gene discovery through expressed sequence tag data mining: Discovery of new human transporter genes ⬇️

A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences

An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases

Annotating Enzymes of Uncertain Function: The Deacylation of d -Amino Acids by Members of the Amidohydrolase Superfamily ,

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug and Play” Domain

Automated discovery of 3D motifs for protein function annotation

Barrels in pieces?

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space

Biocuration in the structure-function linkage database: the anatomy of a superfamily

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric-8.

Can sequence determine function?

Changes to NIH Grant System May Backfire

Cloning and expression of functional rabbit muscle creatine kinase in Escherichia coli. Addressing the problem of microheterogeneity

Cloning and functional characterization of a rat renal organic cation transporter isoform (rOCT1A).

Comparison of methods for genomic localization of gene trap sequences

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

Consequences of domain insertion on sequence-structure divergence in a superfold

Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis

Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases

Creatine kinase protein sequence encoded by a cDNA made from Torpedo californica electric organ mRNA.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily

DASP3: identification of protein sequences belonging to functionally relevant groups

Definitions of enzyme function for the structural genomics era.

Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification

Differential use of protease families for invasion by schistosome cercariae

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening

Discovery of new enzymes and metabolic pathways by using structure and genome context

Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor

Divergent evolution in enolase superfamily: strategies for assigning functions

Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity

Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies

Effusion: prediction of protein function from sequence similarity networks

Enzyme (re)design: lessons from natural evolution and computation

Evaluating Functional Annotations of Enzymes Using the Gene Ontology

Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723.

Evolution of Enzymatic Activities in the Enolase Superfamily: Characterization of the (D)-Glucarate/Galactarate Catabolic Pathway in Escherichia coli ⬇️

Evolution of Enzymatic Activities in the Enolase Superfamily: Crystal Structure of (D)-Glucarate Dehydratase from Pseudomonas putida, ⬇️

Evolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms in Two Families of cis , cis -Muconate Lactonizing Enzymes † ‡

Evolution of Enzymatic Activities in the Enolase Superfamily: l -Rhamnonate Dehydratase † ‡

Evolution of an enzyme active site: The structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase ⬇️

Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans

Evolution of enzyme superfamilies

Evolution of function in the "two dinucleotide binding domains" flavoproteins

Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily

Evolutionary constraints on structural similarity in orthologs and paralogs

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

Evolutionary reprograming of protein-protein interaction specificity

Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily

Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions

Expression of Torpedo californica creatine kinase in Escherichia coli and purification from inclusion bodies

Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches.

Glutathione transferases are structural and functional outliers in the thioredoxin fold

Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution

Inference of Functional Properties from Large-scale Analysis of Enzyme Superfamilies ⬇️

Insights into the Mechanism of Catalysis by the P−C Bond-Cleaving Enzyme Phosphonoacetaldehyde Hydrolase Derived from Gene Sequence Analysis and Mutagenesis ⬇️