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Patricia Babbitt, PhD

TitleProfessor
InstitutionUniversity of California San Francisco
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, 2023
    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 Global Health
    Collapse Websites

    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. Yunes JM, Babbitt PC. Effusion: Prediction of Protein Function from Sequence Similarity Networks. Bioinformatics. 2018 Aug 01. PMID: 30084920.
      View in: PubMed
    2. Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry. 2018 Jul 27. PMID: 30052428.
      View in: PubMed
    3. Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol. 2018; 606:1-71. PMID: 30097089.
      View in: PubMed
    4. Fetrow JS, Babbitt PC. New computational approaches to understanding molecular protein function. PLoS Comput Biol. 2018 Apr; 14(4):e1005756. PMID: 29621256.
      View in: PubMed
    5. Davidson R, Baas BJ, Akiva E, Holliday GL, Polacco BJ, LeVieux JA, Pullara CR, Zhang YJ, Whitman CP, Babbitt PC. A global view of structure-function relationships in the tautomerase superfamily. J Biol Chem. 2018 Feb 16; 293(7):2342-2357. PMID: 29184004.
      View in: PubMed
    6. LeVieux JA, Baas BJ, Kaoud TS, Davidson R, Babbitt PC, Zhang YJ, Whitman CP. 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. Arch Biochem Biophys. 2017 12 15; 636:50-56. PMID: 29111295.
      View in: PubMed
    7. Akiva E, Copp JN, Tokuriki N, Babbitt PC. Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proc Natl Acad Sci U S A. 2017 Nov 07; 114(45):E9549-E9558. PMID: 29078300.
      View in: PubMed
    8. 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 approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci. 2017 Apr; 26(4):677-699. PMID: 28054422.
      View in: PubMed
    9. Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput Biol. 2017 Feb; 13(2):e1005284. PMID: 28187133.
      View in: PubMed
    10. 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 (Oxford). 2017 01 01; 2017. PMID: 28605775.
      View in: PubMed
    11. 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 (Oxford). 2017 Jan 01; 2017(1). PMID: 28365730.
      View in: PubMed
    12. Holliday GL, Davidson R, Akiva E, Babbitt PC. Evaluating Functional Annotations of Enzymes Using the Gene Ontology. Methods Mol Biol. 2017; 1446:111-132. PMID: 27812939.
      View in: PubMed
    13. 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, 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
    14. Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, 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
    15. 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. Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha. Plant Cell. 2016 Oct; 28(10):2632-2650. PMID: 27650333.
      View in: PubMed
    16. 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 PC, 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 09 07; 17(1):184. PMID: 27604469.
      View in: PubMed
    17. Akiva E, Babbitt PC. Evolutionary reprograming of protein-protein interaction specificity. Cell. 2015 Oct 22; 163(3):535-7. PMID: 26496596.
      View in: PubMed
    18. Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, 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
    19. 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, 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
    20. 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 PC, Bateman A. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 2015 Jun; 83(6):1005-13. PMID: 25820941.
      View in: PubMed
    21. Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, 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
    22. Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, 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; PMCID: PMC4839199.
      View in: PubMed, PubMed Central
    23. London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, 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
    24. Brown S, Babbitt P. Using the structure-function linkage database to characterize functional domains in enzymes. Curr Protoc Bioinformatics. 2014 Dec 12; 48:2.10.1-16. PMID: 25501940; PMCID: PMC4349220.
      View in: PubMed, PubMed Central
    25. Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, 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
    26. Brown SD, Babbitt PC. 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
    27. 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 and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30; 3. PMID: 24980702; PMCID: PMC4113996.
      View in: PubMed, PubMed Central
    28. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, 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
    29. Casey AK, Hicks MA, Johnson JL, Babbitt PC, 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
    30. 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. 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
    31. 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 PC. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. PMID: 24271399; PMCID: PMC3965090.
      View in: PubMed, PubMed Central
    32. 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. 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
    33. Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A. 2013 Sep 03; 110(36):E3381-7. PMID: 23959887; PMCID: PMC3767544.
      View in: PubMed, PubMed Central
    34. Schnoes AM, Ream DC, Thorman AW, Babbitt PC, 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
    35. 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. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 2013 Jun 06; 498(7452):123-6. PMID: 23676670; PMCID: PMC3895326.
      View in: PubMed, PubMed Central
    36. Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, 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
    37. 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 PC, 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
    38. Mashiyama ST, Koupparis K, Caffrey CR, McKerrow JH, Babbitt PC. 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
    39. Barber AE, Babbitt PC. Pythoscape: a framework for generation of large protein similarity networks. Bioinformatics. 2012 Nov 01; 28(21):2845-6. PMID: 22962345; PMCID: PMC3476340.
      View in: PubMed, PubMed Central
    40. 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. 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
    41. Gerlt JA, Babbitt PC, Jacobson MP, Almo SC. Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem. 2012 Jan 02; 287(1):29-34. PMID: 22069326; PMCID: PMC3249080.
      View in: PubMed, PubMed Central
    42. Brown SD, Babbitt PC. Inference of functional properties from large-scale analysis of enzyme superfamilies. J Biol Chem. 2012 Jan 02; 287(1):35-42. PMID: 22069325; PMCID: PMC3249087.
      View in: PubMed, PubMed Central
    43. 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 Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62. PMID: 21999478; PMCID: PMC3238057.
      View in: PubMed, PubMed Central
    44. Hicks MA, Barber AE, Giddings LA, Caldwell J, O'Connor SE, Babbitt PC. 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
    45. 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
    46. Almonacid DE, Babbitt PC. 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
    47. Meng EC, Babbitt PC. 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
    48. Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics. 2011 Feb 01; 27(3):326-33. PMID: 21118823; PMCID: PMC3031030.
      View in: PubMed, PubMed Central
    49. Almonacid DE, Yera ER, Mitchell JB, Babbitt PC. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol. 2010 Mar 12; 6(3):e1000700. PMID: 20300652; PMCID: PMC2837397.
      View in: PubMed, PubMed Central
    50. Schnoes AM, Brown SD, Dodevski I, Babbitt PC. 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
    51. Atkinson HJ, Babbitt PC. 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
    52. Atkinson HJ, Babbitt PC, 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
    53. Atkinson HJ, Babbitt PC. 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
    54. Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt PC. 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
    55. Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, 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.
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    56. 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. SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis. 2009 Jun 02; 3(6):e449. PMID: 19488406; PMCID: PMC2685030.
      View in: PubMed, PubMed Central
    57. Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, 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
    58. 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
    59. 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. 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.
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    60. Gerlt JA, Babbitt PC. 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
    61. 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, 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
    62. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. 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
    63. Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, 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
    64. Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, 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
    65. Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, 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.
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    66. Chiang RA, Sali A, Babbitt PC. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol. 2008 Aug 01; 4(8):e1000142. PMID: 18670595; PMCID: PMC2453236.
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    67. Yoshikuni Y, Dietrich JA, Nowroozi FF, Babbitt PC, 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.
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    68. Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt PC, 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.
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    69. Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, 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.
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    70. 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. Differential use of protease families for invasion by schistosome cercariae. Biochimie. 2008 Feb; 90(2):345-58. PMID: 17936488.
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    71. 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. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One. 2007 Jul 18; 2(7):e617. PMID: 17637833; PMCID: PMC1910612.
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    72. Morris JH, Huang CC, Babbitt PC, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 01; 23(17):2345-7. PMID: 17623706.
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    73. Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, 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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    74. Ojha S, Meng EC, Babbitt PC. 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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    75. Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, 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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    76. Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. 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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    77. Glasner ME, Gerlt JA, Babbitt PC. 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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    78. Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC. Comparison of methods for genomic localization of gene trap sequences. BMC Genomics. 2006 Sep 18; 7:236. PMID: 16982004; PMCID: PMC1617135.
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    79. Glasner ME, Gerlt JA, Babbitt PC. Evolution of enzyme superfamilies. Curr Opin Chem Biol. 2006 Oct; 10(5):492-7. PMID: 16935022.
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    80. Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. 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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    81. 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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    82. Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, 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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    83. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. 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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    84. Brown SD, Gerlt JA, Seffernick JL, Babbitt PC. A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol. 2006; 7(1):R8. PMID: 16507141; PMCID: PMC1431709.
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    85. Polacco BJ, Babbitt PC. Automated discovery of 3D motifs for protein function annotation. Bioinformatics. 2006 Mar 15; 22(6):723-30. PMID: 16410325.
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    86. 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. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D642-8. PMID: 16381950; PMCID: PMC1347459.
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    87. Gerlt JA, Babbitt PC, Rayment I. Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys. 2005 Jan 01; 433(1):59-70. PMID: 15581566.
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    88. Babbitt PC, 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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    89. Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput. 2005; 358-69. PMID: 15759641.
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    90. Copley SD, Novak WR, Babbitt PC. Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry. 2004 Nov 09; 43(44):13981-95. PMID: 15518547.
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    91. Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC. Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase. Biochemistry. 2004 Nov 02; 43(43):13766-74. PMID: 15504039.
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    92. Meng EC, Polacco BJ, Babbitt PC. Superfamily active site templates. Proteins. 2004 Jun 01; 55(4):962-76. PMID: 15146493.
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    93. Pegg SC, Novak WR, Babbitt PC. Intersect: identification and visualization of overlaps in database search results. Bioinformatics. 2003 Oct 12; 19(15):1997-9. PMID: 14555634.
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    94. Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, 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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    95. Babbitt PC. 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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    96. McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, 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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    97. Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. The Structure Superposition Database. Nucleic Acids Res. 2003 Jan 01; 31(1):505-10. PMID: 12520064; PMCID: PMC165574.
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    98. 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. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res. 2003 Jan 01; 31(1):278-81. PMID: 12520002; PMCID: PMC165511.
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    99. Brown S, Chang JL, Sadée W, Babbitt PC. 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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    100. Lahiri SD, Wang PF, Babbitt PC, 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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    101. Wang PF, Novak WR, Cantwell JS, Babbitt PC, 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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    102. Wise E, Yew WS, Babbitt PC, 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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    103. Babbitt PC. 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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    104. 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. 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.
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