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Patricia Babbitt, PhD

TitleProfessor
SchoolUCSF School of Pharmacy
DepartmentBioengineering
Address1700 4th Street
San Francisco CA 94158
Phone415-476-3784
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    Collapse Biography 
    Collapse Education and Training
    University of California, San FranciscoPh.D.1988 Graduate Division (Pharmaceutical Chemistry)

    Collapse Overview 
    Collapse Overview
    My laboratory uses computational approaches to improve understanding of how nature has evolved enzymes to catalyze many different chemical reactions by re-using ancestral structures and active site architectures. We created the Structure-Function Linkage Database (SFLD) (http://sfld.rbvi.ucsf.edu) to provide users with access to this information along with tools for analyzing and exploring it. Applications of this work include annotation and prediction of function for new sequences from genome projects and guidance for "rational protein design."


    Collapse Research 
    Collapse Research Activities and Funding
    DECIPHERING ENZYME SPECIFICITY
    NIH P01GM071790Jul 10, 2004 - Jun 30, 2014
    Role: Co-Investigator
    BMI Bioinformatics Training Grant
    NIH/NIGMS T32GM067547Jul 1, 2003 - Jun 30, 2018
    Role: Co-Principal Investigator
    Laying the Foundation of Genomic Enzymology
    NIH/NIGMS R01GM060595Mar 1, 2000 - Apr 30, 2019
    Role: Principal Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse Global Health

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Knutson ST, Westwood BM, Leuthaeuser JB, Turner B, Nguyendac D, Shea G, Kumar K, Hayden J, Harper A, Brown SD, Morris JH, Ferrin TE, Babbitt P, Fetrow JS. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci. 2017 Jan 05. PMID: 28054422.
      View in: PubMed
    2. Finn RD, Attwood TK, Babbitt P, 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, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 Jan 04; 45(D1):D190-D199. PMID: 27899635.
      View in: PubMed
    3. Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt P, Fetrow JS. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics. 2016 Nov 11; 17(1):458. PMID: 27835946.
      View in: PubMed
    4. 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 P, Peters RJ, Chen F, Chappell J. Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha. Plant Cell. 2016 Oct; 28(10):2632-2650. PMID: 27650333.
      View in: PubMed
    5. 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, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt P, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 2016; 17(1):184. PMID: 27604469; PMCID: PMC5015320.
      View in: PubMed, PubMed Central
    6. Akiva E, Babbitt P. Evolutionary Reprograming of Protein-Protein Interaction Specificity. Cell. 2015 Oct 22; 163(3):535-7. PMID: 26496596.
      View in: PubMed
    7. Leuthaeuser JB, Knutson ST, Kumar K, Babbitt P, Fetrow JS. Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity. Protein Sci. 2015 Sep; 24(9):1423-39. PMID: 26073648; PMCID: PMC4570537.
      View in: PubMed, PubMed Central
    8. Babbitt P, 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, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database (Oxford). 2015; 2015:bav063. PMID: 26284514; PMCID: PMC4499208.
      View in: PubMed, PubMed Central
    9. 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, Vriend G, Babbitt P, Bateman A. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 2015 Jun; 83(6):1005-13. PMID: 25820941; PMCID: PMC4446195.
      View in: PubMed, PubMed Central
    10. Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt P, Brown S, Lee YS, Almo SC. Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification. Nucleic Acids Res. 2015 May 19; 43(9):4602-13. PMID: 25855808; PMCID: PMC4482062.
      View in: PubMed, PubMed Central
    11. Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt P, Peters JW, Shepard EM, Broderick JB. [FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. Biochemistry. 2015 Mar 10; 54(9):1807-18. PMID: 25654171.
      View in: PubMed
    12. London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt P, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry. 2015 Jan 20; 54(2):528-37. PMID: 25513739; PMCID: PMC4303301 [Available on 12/16/15].
      View in: PubMed, PubMed Central
    13. Brown S, Babbitt P. Using the structure-function linkage database to characterize functional domains in enzymes. Curr Protoc Bioinformatics. 2014; 48:2.10.1-2.10.16. PMID: 25501940; PMCID: PMC4349220 [Available on 12/12/15].
      View in: PubMed, PubMed Central
    14. Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt P, Poulter CD, Jacobson MP. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. PLoS Comput Biol. 2014 Oct; 10(10):e1003874. PMID: 25299649; PMCID: PMC4191879.
      View in: PubMed, PubMed Central
    15. Brown SD, Babbitt P. New insights about enzyme evolution from large scale studies of sequence and structure relationships. J Biol Chem. 2014 Oct 31; 289(44):30221-8. PMID: 25210038; PMCID: PMC4215206.
      View in: PubMed, PubMed Central
    16. 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 P, Almo SC, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014; 3. PMID: 24980702; PMCID: PMC4113996.
      View in: PubMed, PubMed Central
    17. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt P, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. PMID: 24802635; PMCID: PMC4068255.
      View in: PubMed, PubMed Central
    18. 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 P. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol. 2014 Apr; 12(4):e1001843. PMID: 24756107; PMCID: PMC3995644.
      View in: PubMed, PubMed Central
    19. Casey AK, Hicks MA, Johnson JL, Babbitt P, Frantom PA. Mechanistic and bioinformatic investigation of a conserved active site helix in a-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. Biochemistry. 2014 May 13; 53(18):2915-25. PMID: 24720347; PMCID: PMC4025573.
      View in: PubMed, PubMed Central
    20. 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 P. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. PMID: 24271399; PMCID: PMC3965090.
      View in: PubMed, PubMed Central
    21. Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt P, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 2013 Oct 31; 502(7473):698-702. PMID: 24056934; PMCID: PMC3966649.
      View in: PubMed, PubMed Central
    22. Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt P, Xia Y, Allen KN. Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A. 2013 Sep 3; 110(36):E3381-7. PMID: 23959887; PMCID: PMC3767544.
      View in: PubMed, PubMed Central
    23. Schnoes AM, Ream DC, Thorman AW, Babbitt P, Friedberg I. Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Comput Biol. 2013; 9(5):e1003063. PMID: 23737737; PMCID: PMC3667760.
      View in: PubMed, PubMed Central
    24. Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt P, Jacobson MP, Lee YS, Almo SC. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 2013 Jun 6; 498(7452):123-6. PMID: 23676670; PMCID: PMC3895326.
      View in: PubMed, PubMed Central
    25. Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt P, Almo SC, Jacobson MP, Poulter CD. Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc Natl Acad Sci U S A. 2013 Mar 26; 110(13):E1196-202. PMID: 23493556; PMCID: PMC3612614.
      View in: PubMed, PubMed Central
    26. 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, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt P, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013 Mar; 10(3):221-7. PMID: 23353650; PMCID: PMC3584181.
      View in: PubMed, PubMed Central
    27. Mashiyama ST, Koupparis K, Caffrey CR, McKerrow JH, Babbitt P. A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. PLoS Negl Trop Dis. 2012; 6(12):e1942. PMID: 23236535; PMCID: PMC3516576.
      View in: PubMed, PubMed Central
    28. Barber AE, Babbitt P. Pythoscape: a framework for generation of large protein similarity networks. Bioinformatics. 2012 Nov 1; 28(21):2845-6. PMID: 22962345; PMCID: PMC3476340.
      View in: PubMed, PubMed Central
    29. Crawford ED, Seaman JE, Barber AE, David DC, Babbitt P, Burlingame AL, Wells JA. Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. Cell Death Differ. 2012 Dec; 19(12):2040-8. PMID: 22918439; PMCID: PMC3504717.
      View in: PubMed, PubMed Central
    30. 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 P, Almo SC, Gerlt JA, Jacobson MP. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A. 2012 Mar 13; 109(11):4122-7. PMID: 22392983; PMCID: PMC3306705.
      View in: PubMed, PubMed Central
    31. Gerlt JA, Babbitt P, Jacobson MP, Almo SC. Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem. 2012 Jan 2; 287(1):29-34. PMID: 22069326; PMCID: PMC3249080.
      View in: PubMed, PubMed Central
    32. Brown SD, Babbitt P. Inference of functional properties from large-scale analysis of enzyme superfamilies. J Biol Chem. 2012 Jan 2; 287(1):35-42. PMID: 22069325; PMCID: PMC3249087.
      View in: PubMed, PubMed Central
    33. Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt P, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62. PMID: 21999478; PMCID: PMC3238057.
      View in: PubMed, PubMed Central
    34. Hicks MA, Barber AE, Giddings LA, Caldwell J, O'Connor SE, Babbitt P. The evolution of function in strictosidine synthase-like proteins. Proteins. 2011 Nov; 79(11):3082-98. PMID: 21948213; PMCID: PMC3561908.
      View in: PubMed, PubMed Central
    35. Shen Y, Lee HY, Rawson J, Ojha S, Babbitt P, Fu YH, Ptácek LJ. Mutations in PNKD causing paroxysmal dyskinesia alters protein cleavage and stability. Hum Mol Genet. 2011 Jun 15; 20(12):2322-32. PMID: 21487022; PMCID: PMC3098736.
      View in: PubMed, PubMed Central
    36. Almonacid DE, Babbitt P. Toward mechanistic classification of enzyme functions. Curr Opin Chem Biol. 2011 Jun; 15(3):435-42. PMID: 21489855; PMCID: PMC3551611.
      View in: PubMed, PubMed Central
    37. Meng EC, Babbitt P. Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies. Curr Opin Struct Biol. 2011 Jun; 21(3):391-7. PMID: 21458983; PMCID: PMC3551608.
      View in: PubMed, PubMed Central
    38. Apeltsin L, Morris JH, Babbitt P, Ferrin TE. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics. 2011 Feb 1; 27(3):326-33. PMID: 21118823; PMCID: PMC3031030.
      View in: PubMed, PubMed Central
    39. Almonacid DE, Yera ER, Mitchell JB, Babbitt P. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol. 2010 Mar; 6(3):e1000700. PMID: 20300652; PMCID: PMC2837397.
      View in: PubMed, PubMed Central
    40. Schnoes AM, Brown SD, Dodevski I, Babbitt P. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol. 2009 Dec; 5(12):e1000605. PMID: 20011109; PMCID: PMC2781113.
      View in: PubMed, PubMed Central
    41. Atkinson HJ, Babbitt P. Glutathione transferases are structural and functional outliers in the thioredoxin fold. Biochemistry. 2009 Nov 24; 48(46):11108-16. PMID: 19842715; PMCID: PMC2778357.
      View in: PubMed, PubMed Central
    42. Atkinson HJ, Babbitt P, Sajid M. The global cysteine peptidase landscape in parasites. Trends Parasitol. 2009 Dec; 25(12):573-81. PMID: 19854678; PMCID: PMC3893884.
      View in: PubMed, PubMed Central
    43. Atkinson HJ, Babbitt P. An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput Biol. 2009 Oct; 5(10):e1000541. PMID: 19851441; PMCID: PMC2757866.
      View in: PubMed, PubMed Central
    44. Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt P. A mapping of drug space from the viewpoint of small molecule metabolism. PLoS Comput Biol. 2009 Aug; 5(8):e1000474. PMID: 19701464; PMCID: PMC2727484.
      View in: PubMed, PubMed Central
    45. Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt P, Almo SC, Raushel FM. Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily. Biochemistry. 2009 Jul 14; 48(27):6469-81. PMID: 19518059; PMCID: PMC2748305.
      View in: PubMed, PubMed Central
    46. Dvorák J, Mashiyama ST, Sajid M, Braschi S, Delcroix M, Schneider EL, McKerrow WH, Bahgat M, Hansell E, Babbitt P, Craik CS, McKerrow JH, Caffrey CR. SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis. 2009; 3(6):e449. PMID: 19488406; PMCID: PMC2685030.
      View in: PubMed, PubMed Central
    47. Figueroa M, Hinrichs MV, Bunster M, Babbitt P, Martinez-Oyanedel J, Olate J. Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric-8. Protein Sci. 2009 Jun; 18(6):1139-45. PMID: 19472323; PMCID: PMC2774424.
      View in: PubMed, PubMed Central
    48. Peterson ME, Chen F, Saven JG, Roos DS, Babbitt P, Sali A. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci. 2009 Jun; 18(6):1306-15. PMID: 19472362; PMCID: PMC2774440.
      View in: PubMed, PubMed Central
    49. 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 P, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes. Biochemistry. 2009 Feb 24; 48(7):1445-53. PMID: 19220063; PMCID: PMC2746992.
      View in: PubMed, PubMed Central
    50. Gerlt JA, Babbitt P. Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol. 2009 Feb; 13(1):10-8. PMID: 19237310; PMCID: PMC2711627.
      View in: PubMed, PubMed Central
    51. 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 P, Sali A. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25. PMID: 19219566; PMCID: PMC2693957.
      View in: PubMed, PubMed Central
    52. Atkinson HJ, Morris JH, Ferrin TE, Babbitt P. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One. 2009; 4(2):e4345. PMID: 19190775; PMCID: PMC2631154.
      View in: PubMed, PubMed Central
    53. Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt P, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE. Changes to NIH grant system may backfire. Science. 2008 Nov 21; 322(5905):1187-8. PMID: 19023064.
      View in: PubMed
    54. Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt P, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov 12; 16(11):1668-77. PMID: 19000819; PMCID: PMC2714228.
      View in: PubMed, PubMed Central
    55. Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt P, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry. 2008 Sep 23; 47(38):9944-54. PMID: 18754693; PMCID: PMC2562705.
      View in: PubMed, PubMed Central
    56. Chiang RA, Sali A, Babbitt P. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol. 2008; 4(8):e1000142. PMID: 18670595; PMCID: PMC2453236.
      View in: PubMed, PubMed Central
    57. Yoshikuni Y, Dietrich JA, Nowroozi FF, Babbitt P, Keasling JD. Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways. Chem Biol. 2008 Jun; 15(6):607-18. PMID: 18559271; PMCID: PMC4030648.
      View in: PubMed, PubMed Central
    58. Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt P, Almo SC, Raushel FM. At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate. Biochemistry. 2008 Jan 29; 47(4):1194-206. PMID: 18171028.
      View in: PubMed
    59. Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt P, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans. Biochemistry. 2007 Nov 13; 46(45):12896-908. PMID: 17944491.
      View in: PubMed
    60. Dvorák J, Mashiyama ST, Braschi S, Sajid M, Knudsen GM, Hansell E, Lim KC, Hsieh I, Bahgat M, Mackenzie B, Medzihradszky KF, Babbitt P, Caffrey CR, McKerrow JH. Differential use of protease families for invasion by schistosome cercariae. Biochimie. 2008 Feb; 90(2):345-58. PMID: 17936488.
      View in: PubMed
    61. Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt P, Doniger SW, Skarnes WC, Young SG, Conklin BR. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One. 2007; 2(7):e617. PMID: 17637833; PMCID: PMC1910612.
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    62. Morris JH, Huang CC, Babbitt P, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 1; 23(17):2345-7. PMID: 17623706.
      View in: PubMed
    63. Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt P, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug; 3(8):486-91. PMID: 17603539.
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    64. Ojha S, Meng EC, Babbitt P. Evolution of function in the "two dinucleotide binding domains" flavoproteins. PLoS Comput Biol. 2007 Jul; 3(7):e121. PMID: 17658942; PMCID: PMC1924876.
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    65. Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt P, Almo SC, Raushel FM. Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase. Biochemistry. 2007 Jul 10; 46(27):7953-62. PMID: 17567048.
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    66. Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt P. Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry. 2007 Jun 12; 46(23):6688-95. PMID: 17503785.
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    67. Glasner ME, Gerlt JA, Babbitt P. Mechanisms of protein evolution and their application to protein engineering. Adv Enzymol Relat Areas Mol Biol. 2007; 75:193-239, xii-xiii. PMID: 17124868.
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    68. Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt P. Comparison of methods for genomic localization of gene trap sequences. BMC Genomics. 2006; 7:236. PMID: 16982004; PMCID: PMC1617135.
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    69. Glasner ME, Gerlt JA, Babbitt P. Evolution of enzyme superfamilies. Curr Opin Chem Biol. 2006 Oct; 10(5):492-7. PMID: 16935022.
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    70. Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt P. Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol. 2006 Jun 30; 360(1):228-50. PMID: 16740275.
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    71. Brown S, Babbitt P. Using the Structure-function Linkage Database to characterize functional domains in enzymes. Curr Protoc Bioinformatics. 2006 Mar; Chapter 2:Unit 2.10. PMID: 18428763.
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    72. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt P. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry. 2006 Feb 28; 45(8):2545-55. PMID: 16489747.
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    73. Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt P, Almo SC, Gerlt JA. D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily. Biochemistry. 2006 Feb 28; 45(8):2493-503. PMID: 16489742.
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    74. Brown SD, Gerlt JA, Seffernick JL, Babbitt P. A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol. 2006; 7(1):R8. PMID: 16507141; PMCID: PMC1431709.
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    75. Polacco BJ, Babbitt P. Automated discovery of 3D motifs for protein function annotation. Bioinformatics. 2006 Mar 15; 22(6):723-30. PMID: 16410325.
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    76. 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 P, Ferrin TE. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D642-8. PMID: 16381950; PMCID: PMC1347459.
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    77. Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt P. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput. 2005; 358-69. PMID: 15759641.
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    78. Gerlt JA, Babbitt P, Rayment I. Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys. 2005 Jan 1; 433(1):59-70. PMID: 15581566.
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    79. Babbitt P, Bourne PE, Mooney SD. Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Pac Symp Biocomput. 2005; 319-21. PMID: 15759637.
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    80. Copley SD, Novak WR, Babbitt P. Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry. 2004 Nov 9; 43(44):13981-95. PMID: 15518547.
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    81. Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt P. Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase. Biochemistry. 2004 Nov 2; 43(43):13766-74. PMID: 15504039.
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    82. Meng EC, Polacco BJ, Babbitt P. Superfamily active site templates. Proteins. 2004 Jun 1; 55(4):962-76. PMID: 15146493.
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    83. Pegg SC, Novak WR, Babbitt P. Intersect: identification and visualization of overlaps in database search results. Bioinformatics. 2003 Oct 12; 19(15):1997-9. PMID: 14555634.
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    84. Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt P, Minshull J, Gerlt JA. Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry. 2003 Jul 22; 42(28):8387-93. PMID: 12859183.
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    85. Babbitt P. Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol. 2003 Apr; 7(2):230-7. PMID: 12714057.
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    86. McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt P, Gerlt JA, Kenyon GL. Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633. J Bacteriol. 2003 Apr; 185(8):2451-6. PMID: 12670968; PMCID: PMC152609.
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    87. Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt P. The Structure Superposition Database. Nucleic Acids Res. 2003 Jan 1; 31(1):505-10. PMID: 12520064; PMCID: PMC165574.
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    88. Brown S, Chang JL, Sadée W, Babbitt P. A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes. AAPS PharmSci. 2003; 5(1):E1. PMID: 12713273; PMCID: PMC2751469.
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    89. 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 P, Ferrin TE. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res. 2003 Jan 1; 31(1):278-81. PMID: 12520002; PMCID: PMC165511.
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    90. Lahiri SD, Wang PF, Babbitt P, McLeish MJ, Kenyon GL, Allen KN. The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg(2+)-NO(3)(-)-creatine transition-state analogue complex. Biochemistry. 2002 Nov 26; 41(47):13861-7. PMID: 12437342.
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    91. Wang PF, Novak WR, Cantwell JS, Babbitt P, McLeish MJ, Kenyon GL. Expression of Torpedo californica creatine kinase in Escherichia coli and purification from inclusion bodies. Protein Expr Purif. 2002 Oct; 26(1):89-95. PMID: 12356475.
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    92. Wise E, Yew WS, Babbitt P, Gerlt JA, Rayment I. Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2002 Mar 26; 41(12):3861-9. PMID: 11900527.
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    93. Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AL, Babbitt P. Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches. J Biol Chem. 2001 Jul 27; 276(30):28327-39. PMID: 11309374.
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    94. Cantwell JS, Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt P. Mutagenesis of two acidic active site residues in human muscle creatine kinase: implications for the catalytic mechanism. Biochemistry. 2001 Mar 13; 40(10):3056-61. PMID: 11258919.
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    95. Gerlt JA, Babbitt P. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem. 2001; 70:209-46. PMID: 11395407.
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    96. Gerlt JA, Babbitt P. Barrels in pieces? Nat Struct Biol. 2001 Jan; 8(1):5-7. PMID: 11135656.
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    97. Banatao DR, Huang CC, Babbitt P, Altman RB, Klein TE. ViewFeature: integrated feature analysis and visualization. Pac Symp Biocomput. 2001; 240-50. PMID: 11262944.
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    98. Gerlt JA, Babbitt P. Can sequence determine function? Genome Biol. 2000; 1(5):REVIEWS0005. PMID: 11178260; PMCID: PMC138884.
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    99. Babbitt P. Reengineering the glutathione S-transferase scaffold: a rational design strategy pays off. Proc Natl Acad Sci U S A. 2000 Sep 12; 97(19):10298-300. PMID: 10984526; PMCID: PMC34038.
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    100. Babbitt P, Gerlt JA. New functions from old scaffolds: how nature reengineers enzymes for new functions. Adv Protein Chem. 2000; 55:1-28. PMID: 11050931.
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    101. Huang CC, Novak WR, Babbitt P, Jewett AI, Ferrin TE, Klein TE. Integrated tools for structural and sequence alignment and analysis. Pac Symp Biocomput. 2000; 230-41. PMID: 10902172.
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    102. Chen LH, White CB, Babbitt P, McLeish MJ, Kenyon GL. A comparative study of human muscle and brain creatine kinases expressed in Escherichia coli. J Protein Chem. 2000 Jan; 19(1):59-66. PMID: 10882173.
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    103. Pegg SC, Babbitt P. Shotgun: getting more from sequence similarity searches. Bioinformatics. 1999 Sep; 15(9):729-40. PMID: 10498773.
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    104. Xu L, Resing K, Lawson SL, Babbitt P, Copley SD. Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723. Biochemistry. 1999 Jun 15; 38(24):7659-69. PMID: 10387005.
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    105. Palmer DR, Garrett JB, Sharma V, Meganathan R, Babbitt P, Gerlt JA. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry. 1999 Apr 6; 38(14):4252-8. PMID: 10194342.
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    106. Gulick AM, Palmer DR, Babbitt P, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida. Biochemistry. 1998 Oct 13; 37(41):14358-68. PMID: 9772161.
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    107. Hubbard BK, Koch M, Palmer DR, Babbitt P, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry. 1998 Oct 13; 37(41):14369-75. PMID: 9772162.
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    108. Gerlt JA, Babbitt P. Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis. Curr Opin Chem Biol. 1998 Oct; 2(5):607-12. PMID: 9818186.
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    109. Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt P, Gerlt JA, Petsko GA, Ringe D. Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase. Proc Natl Acad Sci U S A. 1998 Sep 1; 95(18):10396-401. PMID: 9724714; PMCID: PMC27905.
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    110. Baker AS, Ciocci MJ, Metcalf WW, Kim J, Babbitt P, Wanner BL, Martin BM, Dunaway-Mariano 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 Jun 30; 37(26):9305-15. PMID: 9649311.
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    111. Babbitt P, Gerlt JA. Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities. J Biol Chem. 1997 Dec 5; 272(49):30591-4. PMID: 9388188.
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    112. Zhang L, Dresser MJ, Chun JK, Babbitt P, Giacomini KM. Cloning and functional characterization of a rat renal organic cation transporter isoform (rOCT1A). J Biol Chem. 1997 Jun 27; 272(26):16548-54. PMID: 9195965.
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    113. Babbitt P, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA. The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry. 1996 Dec 24; 35(51):16489-501. PMID: 8987982.
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    114. McCarthy DL, Navarrete S, Willett WS, Babbitt P, Copley SD. Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry. 1996 Nov 19; 35(46):14634-42. PMID: 8931562.
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    115. Wood TD, Chen LH, White CB, Babbitt P, Kenyon GL, McLafferty FW. 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; 93(21):12051.
    116. White CB, Chen Q, Kenyon GL, Babbitt P. A novel activity of OmpT. Proteolysis under extreme denaturing conditions. J Biol Chem. 1995 Jun 2; 270(22):12990-4. PMID: 7768890.
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    117. Babbitt P, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA. A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids. Science. 1995 Feb 24; 267(5201):1159-61. PMID: 7855594.
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    118. Dunaway-Mariano D, Babbitt P. On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway. Biodegradation. 1994 Dec; 5(3-4):259-76. PMID: 7765837.
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    119. Mitra B, Gerlt JA, Babbitt P, Koo CW, Kenyon GL, Joseph D, Petsko GA. 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 Dec 7; 32(48):12959-67. PMID: 8241149.
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    120. Williams SE, Woolridge EM, Ransom SC, Landro JA, Babbitt P, Kozarich JW. 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 Oct 13; 31(40):9768-76. PMID: 1390752.
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    121. White KC, Babbitt P, Buechter DD, Kenyon GL. The principal islet of the Coho salmon (Oncorhyncus kisutch) contains the BB isoenzyme of creatine kinase. J Protein Chem. 1992 Oct; 11(5):489-94. PMID: 1449598.
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    122. Babbitt P, Kenyon GL, Martin BM, Charest H, Slyvestre M, Scholten JD, Chang KH, Liang PH, Dunaway-Mariano D. 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 Jun 23; 31(24):5594-604. PMID: 1351742.
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    123. Scholten JD, Chang KH, Babbitt P, Charest H, Sylvestre M, Dunaway-Mariano D. Novel enzymic hydrolytic dehalogenation of a chlorinated aromatic. Science. 1991 Jul 12; 253(5016):182-5. PMID: 1853203.
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    124. Chen LH, Babbitt P, Vásquez JR, West BL, Kenyon GL. Cloning and expression of functional rabbit muscle creatine kinase in Escherichia coli. Addressing the problem of microheterogeneity. J Biol Chem. 1991 Jun 25; 266(18):12053-7. PMID: 2050699.
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    125. Pocalyko DJ, Carroll LJ, Martin BM, Babbitt P, Dunaway-Mariano D. 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 Dec 4; 29(48):10757-65. PMID: 2176881.
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    126. Tsou AY, Ransom SC, Gerlt JA, Buechter DD, Babbitt P, Kenyon GL. 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 Oct 23; 29(42):9856-62. PMID: 2271624.
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    127. Babbitt P, West BL, Buechter DD, Kuntz ID, 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. Biotechnology (N Y). 1990 Oct; 8(10):945-9. PMID: 1370005.
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    128. West BL, Babbitt P, Mendez B, Baxter JD. Creatine kinase protein sequence encoded by a cDNA made from Torpedo californica electric organ mRNA. Proc Natl Acad Sci U S A. 1984 Nov; 81(22):7007-11. PMID: 6594677; PMCID: PMC392065.
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