Publications:
Jump to Year: 2007 2006 2005 2004 2003 2002 2001 2000 1999 pre-1999
Evolution of Enzymatic Activities in the Enolase Superfamily: d-Mannonate Dehydratase from Novosphingobium aromaticivorans.Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA.
Biochemistry. (2007) Nov 13;46(45):12896-12908.
Differential use of protease families for invasion by schistosome cercariae.
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.
Biochimie. (2007) Sep 8; [Epub ahead of print]
Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins.
Ojha S, Meng EC, Babbitt PC.
PLoS Comput Biol. (2007) Jul 20;3(7):e121 [Epub ahead of print]
Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.
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.
PLoS ONE. (2007) Jul 18;2(7):e617.
structureViz: linking Cytoscape and UCSF Chimera.
Morris JH, Huang CC, Babbitt PC, Ferrin TE.
Bioinformatics. (2007) Sep 1;23(17):2345-7.
Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA.
Nat Chem Biol. (2007) Aug;3(8):486-91.
Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.
Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM.
Biochemistry. (2007) Jul 10;46(27):7953-62.
Stability for function trade-offs in the enolase superfamily "catalytic module".
Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC.
Biochemistry. (2007) Jun 12;46(23):6688-95.
Mechanisms of protein evolution and their application to protein engineering.
Glasner ME, Gerlt JA, Babbitt PC.
Adv Enzymol Relat Areas Mol Biol. (2007) 75:193-239, xii-xiii. Review.
back to top
Evolution of enzyme superfamilies.Glasner ME, Gerlt JA, Babbitt PC.
Curr Opin Chem Biol. (2006) Oct;10(5):492-7.
Comparison of methods for genomic localization of gene trap sequences.
Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC.
BMC Genomics. (2006) Sep 18;7:236.
Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.
Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC.
J Mol Biol. (2006) Jun 30;360(1):228-50.
Automated discovery of 3D motifs for protein function annotation.
Polacco BJ, Babbitt PC.
Bioinformatics. (2006) Mar 15;22(6):723-30.
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.
Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC.
Biochemistry. (2006) Feb 28;45(8):2545-55.
D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily.
Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA.
Biochemistry. (2006) Feb 28;45(8):2493-503.
A gold standard set of mechanistically diverse enzyme superfamilies.
Brown SD, Gerlt JA, Seffernick JL, Babbitt PC.
Genome Biol. (2006) 7(1):R8.
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
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, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE.
Nucleic Acids Res. (2006) Jan 1;34(Database issue):D642-8.
back to top
Representing structure-function relationships in mechanistically diverse enzyme superfamilies.Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC.
Pac Symp Biocomput. (2005) 358-69.
Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure.
Babbitt PC, Bourne PE, Mooney SD.
Pac Symp Biocomput. (2005) 319-21.
Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity.
Gerlt JA, Babbitt PC, Rayment I.
Arch Biochem Biophys. (2005) Jan 1;433(1):59-70.
back to top
Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor.Copley SD, Novak WR, Babbitt PC.
Biochemistry. (2004) Nov 9;43(44):13981-95.
Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase.
Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC.
Biochemistry. (2004) Nov 2;43(43):13766-74.
Superfamily active site templates.
Meng EC, Polacco BJ, Babbitt PC.
Proteins. (2004) Jun 1;55(4):962-76.
back to top
Intersect: identification and visualization of overlaps in database search results.Pegg SC, Novak WR, Babbitt PC.
Bioinformatics. (2003) Oct 12;19(15):1997-9.
Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily.
Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA.
Biochemistry. (2003) Jul 22;42(28):8387-93.
Definitions of enzyme function for the structural genomics era.
Babbitt PC.
Curr Opin Chem Biol. (2003) Apr;7(2):230-7.
Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.
McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, Kenyon GL.
J Bacteriol. (2003) Apr;185(8):2451-6.
The Structure Superposition Database.
Chiang, R.A, Meng, E.C., Huang, C.C., Thomas E. Ferrin, T.E., & Babbitt, P.C.
Nuc. Acids Res. 31 (2003) 505-510.
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.
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.
Nucleic Acids Res. (2003) Jan 1;31(1):278-81.
A Semiautomated Approach to Gene Discovery Through Expressed Sequence Tag Data Mining: Discovery of New Human Transporter Genes.
Brown S, Chang JL, Sadee W, Babbitt PC.
AAPS PharmSci; (2003) - 5(1) article 1
back to top
Homologous (/) 8-Barrel Enzymes That Catalyze Unrelated Reactions: Orotidine 5'-Monophosphate Decarboxylase and 3-Keto-L-Gulonate 6-Phosphate Decarboxylase.Eric Wise, Wen Shan Yew, Patricia C. Babbitt, John A. Gerlt, and Ivan Rayment.
Biochem. 41 (2002) 3861-3869.
The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg(2+)-NO(3)(-)-creatine transition-state analogue complex.
Lahiri SD, Wang PF, Babbitt PC, McLeish MJ, Kenyon GL, Allen KN.
Biochemistry. (2002) Nov 26;41(47):13861-7.
Expression of Torpedo californica creatine kinase in Escherichia coli and purification from inclusion bodies.
Wang PF, Novak WR, Cantwell JS, Babbitt PC, McLeish MJ, Kenyon GL.
Protein Expr Purif. (2002) Oct;26(1):89-95.
back to top
Barrels in pieces?John A. Gerlt and Patricia C. Babbitt.
Nature Structural Biology 8 (2001) 5-7.
Mutagenesis of two acidic active site residues in human muscle creatine kinase: Implications for the catalytic mechanism.
John S. Cantwell, Walter R. Novak, Pan-Fen Wang, Michael J. McLeish, George L. Kenyon, and Patricia C. Babbitt.
Biochem. 40 (2001) 3056-3061.
Functional assignment of the 20S Proteasome from T. brucei using mass spectrometry and new bioinformatics approaches.
Lan Huang, Richard J. Jacob, Scott C.-H. Pegg, Michael A. Baldwin, C.C. Wang, A.L. Burlingame, Patricia C. Babbitt.
Jour. Biol. Chem. 276 (2001) 28327-28339.
Divergent Evolution of Enzymatic Function: Mechanistically Diverse Superfamilies and Functionally Distinct Suprafamilies.
Gerlt, J.A. & Babbitt, P.C.
Ann. Rev. of Biochem. 70 (2001) 209-246.
ViewFEATURE: Integrated FEATURE analysis and visualization.
D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, & Teri E. Klein.
Pacific Symposium on Biocomputing Vol. 6, Edited by Russell B. Altman, Teri E. Klein, A. Keith Dunker, and Lawrence Hunter. World Interscience, Singapore, (2001).
back to top
A comparative study of human muscle and brain creatine kinases expressed in E. coli.Lorenzo H. Chen, Camille B. White, Patricia C. Babbitt, Michael J. McLeish & George L. Kenyon
J. Prot. Chem. 19 (2000) 59-66.
Re-engineering the glutathione S-transferase scaffold: A rational design strategy pays off.
Patricia C. Babbitt. (Commentary)
Proc. Natl. Acad. Sci. USA 97 (2000) 10298-10300.
Can sequence determine function?
John A. Gerlt and Patricia C. Babbitt.
Genome Biology 1 (2000) 0005.1-10.
Integrated Tools for Structural and Sequence Alignment and Analysis.
Conrad C. Huang, Walter R. Novak, Patricia C. Babbitt, Andrew I. Jewett, Thomas E. Ferrin, and Teri E. Klein.
Pacific Symposium on Biocomputing Vol. 5, Edited by Russell B. Altman, Teri E. Klein, A. Keith Dunker, and Lawrence Hunter. World Interscience, Singapore, (2000).
Protein Superfamily Building Methods Comparison.
Kunbin Qu, JunZhu, Scott C.-H. Pegg , Patricia Babbitt.
Currents in Computational Molecular Biology, pp. 139-140. Universal Academy Press, Inc. (2000).
New Functions from Old Scaffolds: How NatureRe-engineers Enzymes for New Functions.
Patricia C. Babbitt & John A. Gerlt.
Evolutionary Approaches to Protein Design, series: Advances in Protein Chemistry, Vol. 55. Edited by Frances H. Arnold, Academic Press, San Diego, CA, (2000) 1-28.
back to top
Evidence that pcpA Encodes 2,6-Dichlorohydroquinone Dioxygenase, the Ring Cleavage Enzyme Required for Pentachlorophenol Degradation in Sphingomonas chlorophenolica Strain ATCC 39723.Ling Xu, Katheryn Resing, Sherry L. Lawson, Patricia C. Babbitt, and Shelley D. Copley.
Biochem. 38 (1999) 7659-7669.
Unexpected divergence of function and sequence in orthologous enzymes: "N-acylamino acid racemase" from Amycolaptosis is o-succinylbenzoate synthase.
David R.J. Palmer, James B. Garrett, R. Meganathan, Patricia C. Babbitt, and John A. Gerlt.
Biochem. 38 (1999) 4252-4258.
Shotgun: getting more from sequence similarity searches.
Scott C-H. Pegg and Patricia C. Babbitt.
Bioinformatics 15 (1999) 729-740.
Structure-Based Sequence Alignment of Mandelate Racemase and Muconate Lactonizing Enzyme: Superposition on Reality.
Miriam S. Hasson, Patricia C. Babbitt, Dagmar Ringe, Gregory A. Petsko and George L. Kenyon.
Enzymatic Mechanisms, pp. 308-316. Edited by P.A. Frey and D. B. Northrup. IOS Press, (1999).
back to top
Insights into the mechanism of catalysis by P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis.Angela S. Baker, Michael J. Ciocci, William W. Metcalf, Jaebong Kim, Patricia C. Babbitt, Barry L. Wanner, Brian M. Martin, and Debra Dunaway-Mariano.
Biochem., 37 (1998), 9305-9315.
Evolution of an enzyme active site: The structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.
Miriam S. Hasson, Ilme Schlichting, Javad Moulai, Kirk Taylor, William Barrett, George L. Kenyon, Patricia C. Babbitt, John A. Gerlt, Gregory A. Petsko, and Dagmar Ringe.
Proc. Natl. Acad. Sci. USA, 95 (1998), 10396-10401.
Evolution of enzymatic activities in the Enolase Superfamily: Characterization of the (D) Glucarate/Galactarate catabolic pathway in Escherichia coli.
Brian K. Hubbard, Marjan Koch, David R. J. Palmer, Patricia C. Babbitt, and John A. Gerlt.
Biochem., 37 (1998) 14369-14375.
Evolution of Enzymatic Activities in the Enolase Superfamily: Crystal Structure of (D) Glucarate Dehydratase from Pseudomonas putida.
Andrew M. Gulick, David R. J. Palmer, Patricia C. Babbitt, John A. Gerlt, and Ivan Rayment.
Biochem., 37 (1998) 14358-14368.
Mechanistically diverse enzyme superfamilies: The importance of chemistry in the evolution of catalysis.
John A. Gerlt and Patricia C. Babbitt.
Cur. Op. Chem. Biol., 2 (1998) 607-612.
Superfamily analysis: Understanding protein function from structure and sequence.
Patricia C. Babbitt and Teri E. Klein.
Encyclopedia Comp Chem, Edited by P.v.R. Schleyer. Wiley Interscience, (1998).
Cloning and functional characterization of a rat renal organic cation transporter isoform.
Lei Zhang, Mark J. Dresser, Joanne K. Chun, Patricia C. Babbitt, and Kathleen M. Giacomini.
J. Biol. Chem. 272 (1997) 16548-16554 .
Understanding enzyme superfamilies: Chemistry as the fundamental determinant in the evolution of new catalytic activities.
Patricia C. Babbitt and John A. Gerlt.
J. Biol. Chem.mini review 272 (1997) 30591-30594.
Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione s-transferase superfamily: Oxidative damage or mutagenesis of cys13 converts tetrachlorohydroquinone dehalogenase into a gluthathione S-transferas e.
Darla L. McCarthy, Sandra Navarrete, W. Scott Willett, Patricia C. Babbitt, and Shelley D. Copley.
Biochem. 35, (1996) 14634-14642.
The enolase superfamily: A general strategy for enzyme-catalyzed abstraction of the ?-protons of carboxylic acids.
Patricia C. Babbitt, Miriam S. Hasson, Joseph E. Wedekind, David R. Palmer, George H. Reed, Ivan Rayment, Dagmar Ringe, George L. Kenyon, and John A. Gerlt.
Biochem. 35, (1996) 16489-16501.
A functionally diverse superfamily that abstracts the alpha-protons of carboxylic acids.
Patricia C. Babbitt, Gregory T. Mrachko, Miriam Sarah Hasson, Gjalt W. Huisman, Roberto Kolter, Dagmar Ringe, Gregory A. Petsko, George L. Kenyon, and John A. Gerlt.
Science 267 (1995) 1159-1161.
A novel activity of OmpT: Proteolysis under extreme denaturing conditions.
Camille Bodley White, Qun Chen, George L. Kenyon, and Patricia C. Babbitt.
J. Biol. Chem. 270 (1995) 12990-12994.
Sequence verification of human creatine kinase (43KD) isozymes by high resolution tandem mass spectrometry.
Troy D. Wood, Lorenzo H. Chen, Camille B. White, Patricia C. Babbitt, George L. Kenyon, and F.W. McLafferty.
Proc. Natl. Acad. Sci. USA 92 (1995) 11451-5.
