Patricia Babbitt, PhD
Professor Emeritus
Bioengineering
School of Pharmacy

Applications of this work include annotation and prediction of function for new sequences from genome projects and guidance for "rational protein design."

• Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer.
  Biochemistry 2019 Baas BJ, Medellin BP, LeVieux JA, de Ruijter M, Zhang YJ, Brown SD, Akiva E, Babbitt PC, Whitman CP
• Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions.
  Methods in enzymology 2019 Copp JN, Anderson DW, Akiva E, Babbitt PC, Tokuriki N
• Effusion: prediction of protein function from sequence similarity networks.
  Bioinformatics (Oxford, England) 2019 Yunes JM, Babbitt PC
• InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
  Nucleic acids research 2019 Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, …
• Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks.
  Biochemistry 2018 Copp JN, Akiva E, Babbitt PC, Tokuriki N
• Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain.
  Methods in enzymology 2018 Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC
• New computational approaches to understanding molecular protein function.
  PLoS computational biology 2018 Fetrow JS, Babbitt PC
• A global view of structure-function relationships in the tautomerase superfamily.
  The Journal of biological chemistry 2017 Davidson R, Baas BJ, Akiva E, Holliday GL, Polacco BJ, LeVieux JA, Pullara CR, Zhang YJ, Whitman CP, Babbitt PC
• 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.
  Archives of biochemistry and biophysics 2017 LeVieux JA, Baas BJ, Kaoud TS, Davidson R, Babbitt PC, Zhang YJ, Whitman CP
• Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Akiva E, Copp JN, Tokuriki N, Babbitt PC
• An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.
  Protein science : a publication of the Protein Society 2017 Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS
• An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.
  PLoS computational biology 2017 Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS
• 3D Motifs.
  From Protein Structure to Function with Bioinformatics 2017 Jerome P. Nilmeier, Elaine C. Meng, Benjamin J. Polacco, Patricia C. Babbitt
• Biocuration in the structure-function linkage database: the anatomy of a superfamily.
  Database : the journal of biological databases and curation 2017 Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC
• Biocuration in the structure-function linkage database: the anatomy of a superfamily.
  Database : the journal of biological databases and curation 2017 Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC
• Evaluating Functional Annotations of Enzymes Using the Gene Ontology.
  Methods in molecular biology (Clifton, N.J.) 2017 Holliday GL, Davidson R, Akiva E, Babbitt PC
• InterPro in 2017-beyond protein family and domain annotations.
  Nucleic acids research 2016 Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A,…
• DASP3: identification of protein sequences belonging to functionally relevant groups.
  BMC bioinformatics 2016 Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS
• Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha.
  The Plant cell 2016 Kumar S, Kempinski C, Zhuang X, Norris A, Mafu S, Zi J, Bell SA, Nybo SE, Kinison SE, Jiang Z, Goklany S, Linscott KB, Chen X, Jia Q, Brown SD, Bowman JL, Babbitt PC, Peters RJ, Chen F, Chappell J
• An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
  Genome biology 2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, …
• Evolutionary reprograming of protein-protein interaction specificity.
  Cell 2015 Akiva E, Babbitt PC
• Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.
  Protein science : a publication of the Protein Society 2015 Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, Fetrow JS
• Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
  Database : the journal of biological databases and curation 2015 Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, …
• Key challenges for the creation and maintenance of specialist protein resources.
  Proteins 2015 Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, …
• Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.
  Nucleic acids research 2015 Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC
• Enzyme ‘Social’ Networks: Tracking Sequence / Function Relationships to Elucidate Determinants of Enzyme Specificity and Mechanism.
  The FASEB Journal 2015 Eyal Akiva, Shoshana Brown, Gemma Holliday, Patricia Babbitt
• [FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis.
  Biochemistry 2015 Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, Peters JW, Shepard EM, Broderick JB
• Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.
  Biochemistry 2015 London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK
• Using the structure-function linkage database to characterize functional domains in enzymes.
  Current protocols in bioinformatics 2014 Brown S, Babbitt P
• Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach.
  PLoS computational biology 2014 Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP
• New insights about enzyme evolution from large scale studies of sequence and structure relationships.
  The Journal of biological chemistry 2014 Brown SD, Babbitt PC
• Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.
  eLife 2014 Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP
• Prediction of substrates for glutathione transferases by covalent docking.
  Journal of chemical information and modeling 2014 Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A
• Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere.
  PLoS biology 2014 Mashiyama ST, Malabanan MM, Akiva E, Bhosle R, Branch MC, Hillerich B, Jagessar K, Kim J, Patskovsky Y, Seidel RD, Stead M, Toro R, Vetting MW, Almo SC, Armstrong RN, Babbitt PC
• 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 Casey AK, Hicks MA, Johnson JL, Babbitt PC, Frantom PA
• The Nucleophilic Attack Six-Bladed ß-Propeller (N6P) Superfamily.
  Protein Families 2013 Michael A. Hicks, Alan E. Barber, Patricia C. Babbitt
• The Structure-Function Linkage Database.
  Nucleic acids research 2013 Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt …
• Discovery of new enzymes and metabolic pathways by using structure and genome context.
  Nature 2013 Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP
• Consequences of domain insertion on sequence-structure divergence in a superfold.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN
• Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.
  PLoS computational biology 2013 Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I
• Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.
  Nature 2013 Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC
• The nature of sequence and structure divergence in the Haloalkanoate Dehalogenase SuperFamily (HADSF).
  The FASEB Journal 2013 Chetanya Pandya, Shoshana D Brown, Debra Dunaway-Mariano, Patricia C Babbitt, Yu Xia, Karen N Allen
• Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD
• A large-scale evaluation of computational protein function prediction.
  Nature methods 2013 Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, …
• A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets.
  PLoS neglected tropical diseases 2012 Mashiyama ST, Koupparis K, Caffrey CR, McKerrow JH, Babbitt PC
• Pythoscape: a framework for generation of large protein similarity networks.
  Bioinformatics (Oxford, England) 2012 Barber AE, Babbitt PC
• Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis.
  Cell death and differentiation 2012 Crawford ED, Seaman JE, Barber AE, David DC, Babbitt PC, Burlingame AL, Wells JA
• Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP
• Divergent evolution in enolase superfamily: strategies for assigning functions.
  The Journal of biological chemistry 2011 Gerlt JA, Babbitt PC, Jacobson MP, Almo SC
• Inference of functional properties from large-scale analysis of enzyme superfamilies.
  The Journal of biological chemistry 2011 Brown SD, Babbitt PC
• The Enzyme Function Initiative.
  Biochemistry 2011 Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV
• The evolution of function in strictosidine synthase-like proteins.
  Proteins 2011 Hicks MA, Barber AE, Giddings LA, Caldwell J, O'Connor SE, Babbitt PC
• Mutations in PNKD causing paroxysmal dyskinesia alters protein cleavage and stability.
  Human molecular genetics 2011 Shen Y, Lee HY, Rawson J, Ojha S, Babbitt P, Fu YH, Ptácek LJ
• Toward mechanistic classification of enzyme functions.
  Current opinion in chemical biology 2011 Almonacid DE, Babbitt PC
• Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies.
  Current opinion in structural biology 2011 Meng EC, Babbitt PC
• Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
  Bioinformatics (Oxford, England) 2010 Apeltsin L, Morris JH, Babbitt PC, Ferrin TE
• Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.
  PLoS computational biology 2010 Almonacid DE, Yera ER, Mitchell JB, Babbitt PC
• Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
  PLoS computational biology 2009 Schnoes AM, Brown SD, Dodevski I, Babbitt PC
• Glutathione transferases are structural and functional outliers in the thioredoxin fold.
  Biochemistry 2009 Atkinson HJ, Babbitt PC
• The global cysteine peptidase landscape in parasites.
  Trends in parasitology 2009 Atkinson HJ, Babbitt PC, Sajid M
• An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations.
  PLoS computational biology 2009 Atkinson HJ, Babbitt PC
• A mapping of drug space from the viewpoint of small molecule metabolism.
  PLoS computational biology 2009 Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt PC
• Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily.
  Biochemistry 2009 Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, Almo SC, Raushel FM
• SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni.
  PLoS neglected tropical diseases 2009 Dvorák J, Mashiyama ST, Sajid M, Braschi S, Delcroix M, Schneider EL, McKerrow WH, Bahgat M, Hansell E, Babbitt PC, Craik CS, McKerrow JH, Caffrey CR
• Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric-8.
  Protein science : a publication of the Protein Society 2009 Figueroa M, Hinrichs MV, Bunster M, Babbitt P, Martinez-Oyanedel J, Olate J
• Evolutionary constraints on structural similarity in orthologs and paralogs.
  Protein science : a publication of the Protein Society 2009 Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A
• Evolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms in Two Families of cis , cis -Muconate Lactonizing Enzymes.
  Biochemistry 2009 Ayano Sakai, Alexander A. Fedorov, Elena V. Fedorov, Alexandra M. Schnoes, Margaret E. Glasner, Shoshana Brown, Marc E. Rutter, Kevin Bain, Shawn Chang, Tarun Gheyi, J. Michael Sauder, Stephen K. …
• Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.
  Biochemistry 2009 Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA
• Enzyme (re)design: lessons from natural evolution and computation.
  Current opinion in chemical biology 2009 Gerlt JA, Babbitt PC
• Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
  Journal of structural and functional genomics 2009 Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, …
• Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.
  PloS one 2009 Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC
• 3D Motifs.
  From Protein Structure to Function with Bioinformatics 2009 Elaine C. Meng, Benjamin J. Polacco, Patricia C. Babbitt
• Changes to NIH grant system may backfire.
  Science (New York, N.Y.) 2008 Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE
• Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
  Structure (London, England : 1993) 2008 Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP
• Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.
  Biochemistry 2008 Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA
• Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
  PLoS computational biology 2008 Chiang RA, Sali A, Babbitt PC
• Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways.
  Chemistry & biology 2008 Yoshikuni Y, Dietrich JA, Nowroozi FF, Babbitt PC, Keasling JD
• At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate.
  Biochemistry 2008 Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt PC, Almo SC, Raushel FM
• Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.
  Biochemistry 2007 Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA
• Differential use of protease families for invasion by schistosome cercariae.
  Biochimie 2007 Dvorák J, Mashiyama ST, Braschi S, Sajid M, Knudsen GM, Hansell E, Lim KC, Hsieh I, Bahgat M, Mackenzie B, Medzihradszky KF, Babbitt PC, Caffrey CR, McKerrow JH
• Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.
  PloS one 2007 Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR
• structureViz: linking Cytoscape and UCSF Chimera.
  Bioinformatics (Oxford, England) 2007 Morris JH, Huang CC, Babbitt PC, Ferrin TE
• Evolution of function in the "two dinucleotide binding domains" flavoproteins.
  PLoS computational biology 2007 Ojha S, Meng EC, Babbitt PC
• Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
  Nature chemical biology 2007 Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA
• Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.
  Biochemistry 2007 Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM
• Stability for function trade-offs in the enolase superfamily "catalytic module".
  Biochemistry 2007 Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC
• Mechanisms of protein evolution and their application to protein engineering.
  Advances in enzymology and related areas of molecular biology 2007 Glasner ME, Gerlt JA, Babbitt PC
• Comparison of methods for genomic localization of gene trap sequences.
  BMC genomics 2006 Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC
• Evolution of enzyme superfamilies.
  Current opinion in chemical biology 2006 Glasner ME, Gerlt JA, Babbitt PC
• Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.
  Journal of molecular biology 2006 Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC
• Characterizing the structure-function relationship in the thioredoxin fold class.
  The FASEB Journal 2006 Holly J Atkinson, Patricia C. Babbitt
• Evaluating function in uncharacterized enzymes.
  The FASEB Journal 2006 Alexandra M Schnoes, Igor Dodevski, Patricia C Babbitt
• Evolution of structure and function in the o-succinylbenzoate synthase family.
  The FASEB Journal 2006 Margaret E. Glasner, Nima Fayazmanesh, Ranyee Chiang, Matthew P. Jacobson, John A. Gerlt, Patricia C. Babbitt
• Evolutionary relationships in the glutathione reductase superfamily.
  The FASEB Journal 2006 Sunil Ojha, Elaine Meng, Patricia C Babbitt
• Improving Comparative Structure Modeling through the Use of Multiple Templates.
  The FASEB Journal 2006 Mark Erik Peterson, Patricia C. Babbitt, Andrej Sali
• Investigating the properties of catalytic module residues in the enolase superfamily: Effects on thermostability.
  The FASEB Journal 2006 Ray Jr. Anthony Nagatani, Patricia Clement Babbitt
• The Structure-Function Linkage Database.
  The FASEB Journal 2006 Shoshana Brown, Scott Pegg, Sunil Ojha, Conrad Huang, Thomas E. Ferrin, Patricia C. Babbitt
• Using the Structure-function Linkage Database to characterize functional domains in enzymes.
  Current protocols in bioinformatics 2006 Brown S, Babbitt P
• D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily.
  Biochemistry 2006 Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA
• Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.
  Biochemistry 2006 Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC
• A gold standard set of mechanistically diverse enzyme superfamilies.
  Genome biology 2006 Brown SD, Gerlt JA, Seffernick JL, Babbitt PC
• Automated discovery of 3D motifs for protein function annotation.
  Bioinformatics (Oxford, England) 2006 Polacco BJ, Babbitt PC
• The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
  Nucleic acids research 2006 Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, …
• Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity.
  Archives of biochemistry and biophysics 2005 Gerlt JA, Babbitt PC, Rayment I
• Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005 Babbitt PC, Bourne PE, Mooney SD
• Representing structure-function relationships in mechanistically diverse enzyme superfamilies.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005 Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC
• Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor.
  Biochemistry 2004 Copley SD, Novak WR, Babbitt PC
• Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase.
  Biochemistry 2004 Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC
• Superfamily active site templates.
  Proteins 2004 Meng EC, Polacco BJ, Babbitt PC
• Intersect: identification and visualization of overlaps in database search results.
  Bioinformatics (Oxford, England) 2003 Pegg SC, Novak WR, Babbitt PC
• Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily.
  Biochemistry 2003 Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA
• Definitions of enzyme function for the structural genomics era.
  Current opinion in chemical biology 2003 Babbitt PC
• Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.
  Journal of bacteriology 2003 McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, Kenyon GL
• A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes.
  AAPS pharmSci 2003 Brown S, Chang JL, Sadée W, Babbitt PC
• BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.
  Nucleic acids research 2003 Stryke D, Kawamoto M, Huang CC, Johns SJ, King LA, Harper CA, Meng EC, Lee RE, Yee A, L'Italien L, Chuang PT, Young SG, Skarnes WC, Babbitt PC, Ferrin TE
• The Structure Superposition Database.
  Nucleic acids research 2003 Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC
• Superfamily Analysis: Understanding Protein Function from Structure and Sequence.
  Encyclopedia of Computational Chemistry 2002 Patricia C. Babbitt, Teri E. Klein
• Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase.
  Biochemistry 2002 Wise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I
• Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches.
  The Journal of biological chemistry 2001 Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AL, Babbitt PC
• Mutagenesis of two acidic active site residues in human muscle creatine kinase: implications for the catalytic mechanism.
  Biochemistry 2001 Cantwell JS, Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC
• Barrels in pieces?
  Nature structural biology 2001 Gerlt JA, Babbitt PC
• ViewFeature: integrated feature analysis and visualization.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001 Banatao DR, Huang CC, Babbitt PC, Altman RB, Klein TE
• Can sequence determine function?
  Genome biology 2000 Gerlt JA, Babbitt PC
• Reengineering the glutathione S-transferase scaffold: a rational design strategy pays off.
  Proceedings of the National Academy of Sciences of the United States of America 2000 Babbitt PC
• A comparative study of human muscle and brain creatine kinases expressed in Escherichia coli.
  Journal of protein chemistry 2000 Chen LH, White CB, Babbitt PC, McLeish MJ, Kenyon GL
• Integrated tools for structural and sequence alignment and analysis.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000 Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE
• New functions from old scaffolds: how nature reengineers enzymes for new functions.
  Advances in protein chemistry 2000 Babbitt PC, Gerlt JA
• Shotgun: getting more from sequence similarity searches.
  Bioinformatics (Oxford, England) 1999 Pegg SC, Babbitt PC
• Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723.
  Biochemistry 1999 Xu L, Resing K, Lawson SL, Babbitt PC, Copley SD
• Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase.
  Biochemistry 1999 Palmer DR, Garrett JB, Sharma V, Meganathan R, Babbitt PC, Gerlt JA
• Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli.
  Biochemistry 1998 Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA
• Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
  Biochemistry 1998 Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I
• Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis.
  Current opinion in chemical biology 1998 Gerlt JA, Babbitt PC
• Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.
  Proceedings of the National Academy of Sciences of the United States of America 1998 Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt PC, Gerlt JA, Petsko GA, Ringe D
• Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis.
  Biochemistry 1998 Baker AS, Ciocci MJ, Metcalf WW, Kim J, Babbitt PC, Wanner BL, Martin BM, Dunaway-Mariano D
• Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities.
  The Journal of biological chemistry 1997 Babbitt PC, Gerlt JA
• Cloning and functional characterization of a rat renal organic cation transporter isoform (rOCT1A).
  The Journal of biological chemistry 1997 Zhang L, Dresser MJ, Chun JK, Babbitt PC, Giacomini KM
• The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
  Biochemistry 1996 Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA
• Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily.
  Biochemistry 1996 McCarthy DL, Navarrete S, Willett WS, Babbitt PC, Copley SD
• Sequence verification of human creatine kinase (43 kDa) isozymes by high-resolution tandem mass spectrometry
  Proc Natl Acad Sci U S A. 1995 Dec 5; 92(25):11451-5. Erratum in: Proc Natl Acad Sci U S A 1996 Wood TD, Chen LH, White CB, Babbitt PC, Kenyon GL, McLafferty FW
• Sequence verification of human creatine kinase (43 kDa) isozymes by high-resolution tandem mass spectrometry.
  Proceedings of the National Academy of Sciences of the United States of America 1996 T D Wood, L H Chen, C B White, P C Babbitt, G L Kenyon, F W McLafferty
• A novel activity of OmpT. Proteolysis under extreme denaturing conditions.
  The Journal of biological chemistry 1995 White CB, Chen Q, Kenyon GL, Babbitt PC
• A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids.
  Science (New York, N.Y.) 1995 Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA
• S-MANDEL ATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA: CONSTRUCTION OF A SOLUBLE CHIMERIC MUTANT OF A MEMBRANE-BOUND ENZYME.
  1994 Bharati Mitra, John A. Gerlt, Patricia C. Babbitt, George L. Kenyon, Diane Joseph, Gregory A. Petsko
• On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway.
  Biodegradation 1994 Dunaway-Mariano D, Babbitt PC
• A novel structural basis for membrane association of a protein: construction of a chimeric soluble mutant of (S)-mandelate dehydrogenase from Pseudomonas putida.
  Biochemistry 1993 Mitra B, Gerlt JA, Babbitt PC, Koo CW, Kenyon GL, Joseph D, Petsko GA
• 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.
  Biochemistry 1992 Williams SE, Woolridge EM, Ransom SC, Landro JA, Babbitt PC, Kozarich JW
• The principal islet of the Coho salmon (Oncorhyncus kisutch) contains the BB isoenzyme of creatine kinase.
  Journal of protein chemistry 1992 White KC, Babbitt PC, Buechter DD, Kenyon GL
• 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.
  Biochemistry 1992 Babbitt PC, Kenyon GL, Martin BM, Charest H, Slyvestre M, Scholten JD, Chang KH, Liang PH, Dunaway-Mariano D
• ChemInform Abstract: Novel Enzymic Hydrolytic Dehalogenation of a Chlorinated Aromatic.
  ChemInform 1991 J. D. SCHOLTEN, K.-H. CHANG, P. C. BABBITT, H. CHAREST, M. SYLVESTRE, D. DUNAWAY-MARIANO
• Active Creatine Kinase Refolded from Inclusion Bodies in Escherichia coli.
  Protein Refolding 1991 Patricia C. Babbitt, Brian L. West, Douglas D. Buechter, Lorenzo H. Chen, Irwin D. Kuntz, George L. Kenyon
• Novel enzymic hydrolytic dehalogenation of a chlorinated aromatic.
  Science (New York, N.Y.) 1991 Scholten JD, Chang KH, Babbitt PC, Charest H, Sylvestre M, Dunaway-Mariano D
• Cloning and expression of functional rabbit muscle creatine kinase in Escherichia coli. Addressing the problem of microheterogeneity.
  The Journal of biological chemistry 1991 Chen LH, Babbitt PC, Vásquez JR, West BL, Kenyon GL
• Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs.
  Biochemistry 1990 Pocalyko DJ, Carroll LJ, Martin BM, Babbitt PC, Dunaway-Mariano D
• Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli.
  Biochemistry 1990 Tsou AY, Ransom SC, Gerlt JA, Buechter DD, Babbitt PC, Kenyon GL
• Removal of a proteolytic activity associated with aggregates formed from expression of creatine kinase in Escherichia coli leads to improved recovery of active enzyme.
  Bio/technology (Nature Publishing Company) 1990 Babbitt PC, West BL, Buechter DD, Kuntz ID, Kenyon GL
• Adenosine 5'-[.alpha.,.beta.-imido]triphosphate, a substrate for T7 RNA polymerase and rabbit muscle creatine kinase [Erratum to document cited in CA109(1):6886j].
  Journal of the American Chemical Society 1988 Qi Feng. Ma, Patricia C. Babbitt, George L. Kenyon
• ChemInform Abstract: Adenosine 5'-(a,ß-Imido)triphosphate, a Substrate for T7 RNA Polymerase and Rabbit Muscle Creatine Kinase.
  ChemInform 1988 Q. MA, P. C. BABBITT, G. L. KENYON
• Adenosine 5'-[.alpha.,.beta.-imido]triphosphate, a substrate for T7 RNA polymerase and rabbit muscle creatine kinase.
  Journal of the American Chemical Society 1988 Qi Feng. Ma, Patricia C. Babbitt, George L. Kenyon
• Comparisons of creatine kinase primary structures.
  The Protein Journal 1986 Patricia C. Babbitt, George L. Kenyon, Irwin D. Kuntz, Fred E. Cohen, John D. Baxter, Pamela A. Benfield, Jean D. Buskin, William A. Gilbert, Steven D. Hauschka, Johann P. Hossle, Charles P. Ordahl, …
• Creatine kinase protein sequence encoded by a cDNA made from Torpedo californica electric organ mRNA.
  Proceedings of the National Academy of Sciences of the United States of America 1984 West BL, Babbitt PC, Mendez B, Baxter JD
• Fingerprinting and characterization of carboxylic acids in in-situ oil shale retort and process waters by capillary column gas chromatography-mass spectrometry.
  Fuel 1982 Richard H. Fish, Amos S. Newton, Patricia C. Babbitt