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Patricia Babbitt, PhD

Title(s)Professor Emeritus, Bioengineering
SchoolSchool of Pharmacy
Address1700 4th Street
San Francisco CA 94158
Phone415-502-1248
ORCID ORCID Icon0000-0003-0375-9015 Additional info
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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 - Mar 31, 2010
    Role: Principal Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

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    Collapse Academic Senate

    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer. Biochemistry. 2020 Apr 28; 59(16):1592-1603. Medellin BP, Lancaster EB, Brown SD, Rakhade S, Babbitt PC, Whitman CP, Zhang YJ. PMID: 32242662.
      View in: PubMed   Mentions:    Fields:    
    2. A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database (Oxford). 2020 Jan 01; 2020. Holliday GL, Brown SD, Mischel D, Polacco BJ, Babbitt PC. PMID: 32449511.
      View in: PubMed   Mentions:    Fields:    
    3. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019 11 19; 20(1):244. Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkiran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidovic RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijevic V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. PMID: 31744546.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    4. Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer. Biochemistry. 2019 06 04; 58(22):2617-2627. Baas BJ, Medellin BP, LeVieux JA, de Ruijter M, Zhang YJ, Brown SD, Akiva E, Babbitt PC, Whitman CP. PMID: 31074977.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    5. Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions. Methods Enzymol. 2019; 620:315-347. Copp JN, Anderson DW, Akiva E, Babbitt PC, Tokuriki N. PMID: 31072492.
      View in: PubMed   Mentions: 2     Fields:    
    6. Effusion: prediction of protein function from sequence similarity networks. Bioinformatics. 2019 02 01; 35(3):442-451. Yunes JM, Babbitt PC. PMID: 30084920.
      View in: PubMed   Mentions:    Fields:    
    7. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019 01 08; 47(D1):D351-D360. Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD. PMID: 30398656.
      View in: PubMed   Mentions: 97     Fields:    Translation:HumansAnimalsCells
    8. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry. 2018 08 07; 57(31):4651-4662. Copp JN, Akiva E, Babbitt PC, Tokuriki N. PMID: 30052428.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    9. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol. 2018; 606:1-71. Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. PMID: 30097089.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    10. New computational approaches to understanding molecular protein function. PLoS Comput Biol. 2018 04; 14(4):e1005756. Fetrow JS, Babbitt PC. PMID: 29621256.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    11. A global view of structure-function relationships in the tautomerase superfamily. J Biol Chem. 2018 02 16; 293(7):2342-2357. Davidson R, Baas BJ, Akiva E, Holliday GL, Polacco BJ, LeVieux JA, Pullara CR, Zhang YJ, Whitman CP, Babbitt PC. PMID: 29184004.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    12. 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. LeVieux JA, Baas BJ, Kaoud TS, Davidson R, Babbitt PC, Zhang YJ, Whitman CP. PMID: 29111295.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    13. Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proc Natl Acad Sci U S A. 2017 11 07; 114(45):E9549-E9558. Akiva E, Copp JN, Tokuriki N, Babbitt PC. PMID: 29078300.
      View in: PubMed   Mentions: 11     Fields:    
    14. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci. 2017 04; 26(4):677-699. 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. PMID: 28054422.
      View in: PubMed   Mentions: 3     Fields:    
    15. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput Biol. 2017 02; 13(2):e1005284. Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. PMID: 28187133.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    16. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 01 01; 2017(1). Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. PMID: 28365730.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    17. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 Jan 01; 2017. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. PMID: 28605775.
      View in: PubMed   Mentions: 1     Fields:    
    18. Evaluating Functional Annotations of Enzymes Using the Gene Ontology. Methods Mol Biol. 2017; 1446:111-132. Holliday GL, Davidson R, Akiva E, Babbitt PC. PMID: 27812939.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    19. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 01 04; 45(D1):D190-D199. 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. PMID: 27899635.
      View in: PubMed   Mentions: 305     Fields:    Translation:HumansCells
    20. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics. 2016 Nov 11; 17(1):458. Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. PMID: 27835946.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    21. Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha. Plant Cell. 2016 10; 28(10):2632-2650. 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. PMID: 27650333.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    22. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 2016 09 07; 17(1):184. 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. PMID: 27604469.
      View in: PubMed   Mentions: 55     Fields:    Translation:Humans
    23. Evolutionary reprograming of protein-protein interaction specificity. Cell. 2015 Oct 22; 163(3):535-7. Akiva E, Babbitt PC. PMID: 26496596.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    24. 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. Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, Fetrow JS. PMID: 26073648.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    25. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database (Oxford). 2015; 2015:bav063. 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. PMID: 26284514.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    26. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 2015 Jun; 83(6):1005-13. 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. PMID: 25820941.
      View in: PubMed   Mentions: 5     Fields:    
    27. Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification. Nucleic Acids Res. 2015 May 19; 43(9):4602-13. Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC. PMID: 25855808.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    28. [FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. Biochemistry. 2015 Mar 10; 54(9):1807-18. Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, Peters JW, Shepard EM, Broderick JB. PMID: 25654171.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    29. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry. 2015 Jan 20; 54(2):528-37. London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. PMID: 25513739.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    30. Using the structure-function linkage database to characterize functional domains in enzymes. Curr Protoc Bioinformatics. 2014 Dec 12; 48:2.10.1-16. Brown S, Babbitt P. PMID: 25501940.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    31. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. PLoS Comput Biol. 2014 Oct; 10(10):e1003874. Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. PMID: 25299649.
      View in: PubMed   Mentions: 7     Fields:    
    32. New insights about enzyme evolution from large scale studies of sequence and structure relationships. J Biol Chem. 2014 Oct 31; 289(44):30221-8. Brown SD, Babbitt PC. PMID: 25210038.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    33. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30; 3. 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. PMID: 24980702.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    34. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. PMID: 24802635.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    35. 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. Casey AK, Hicks MA, Johnson JL, Babbitt PC, Frantom PA. PMID: 24720347.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    36. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol. 2014 Apr; 12(4):e1001843. 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. PMID: 24756107.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    37. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. 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. PMID: 24271399.
      View in: PubMed   Mentions: 77     Fields:    
    38. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 2013 Oct 31; 502(7473):698-702. 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. PMID: 24056934.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    39. 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. Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. PMID: 23959887.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    40. 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. Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I. PMID: 23737737.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimals
    41. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 2013 Jun 06; 498(7452):123-6. 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. PMID: 23676670.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    42. 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. Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD. PMID: 23493556.
      View in: PubMed   Mentions: 25     Fields:    
    43. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013 Mar; 10(3):221-7. 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. PMID: 23353650.
      View in: PubMed   Mentions: 234     Fields:    Translation:HumansAnimals
    44. 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. Mashiyama ST, Koupparis K, Caffrey CR, McKerrow JH, Babbitt PC. PMID: 23236535.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    45. Pythoscape: a framework for generation of large protein similarity networks. Bioinformatics. 2012 Nov 01; 28(21):2845-6. Barber AE, Babbitt PC. PMID: 22962345.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    46. 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. 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. PMID: 22392983.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    47. Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem. 2012 Jan 02; 287(1):29-34. Gerlt JA, Babbitt PC, Jacobson MP, Almo SC. PMID: 22069326.
      View in: PubMed   Mentions: 44     Fields:    Translation:Humans
    48. Inference of functional properties from large-scale analysis of enzyme superfamilies. J Biol Chem. 2012 Jan 02; 287(1):35-42. Brown SD, Babbitt PC. PMID: 22069325.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimals
    49. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62. 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. PMID: 21999478.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansAnimalsCells
    50. The evolution of function in strictosidine synthase-like proteins. Proteins. 2011 Nov; 79(11):3082-98. Hicks MA, Barber AE, Giddings LA, Caldwell J, O'Connor SE, Babbitt PC. PMID: 21948213.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    51. Mutations in PNKD causing paroxysmal dyskinesia alters protein cleavage and stability. Hum Mol Genet. 2011 Jun 15; 20(12):2322-32. Shen Y, Lee HY, Rawson J, Ojha S, Babbitt P, Fu YH, Ptácek LJ. PMID: 21487022.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    52. Toward mechanistic classification of enzyme functions. Curr Opin Chem Biol. 2011 Jun; 15(3):435-42. Almonacid DE, Babbitt PC. PMID: 21489855.
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    53. Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies. Curr Opin Struct Biol. 2011 Jun; 21(3):391-7. Meng EC, Babbitt PC. PMID: 21458983.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    54. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics. 2011 Feb 01; 27(3):326-33. Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. PMID: 21118823.
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    55. 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. Almonacid DE, Yera ER, Mitchell JB, Babbitt PC. PMID: 20300652.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    56. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol. 2009 Dec; 5(12):e1000605. Schnoes AM, Brown SD, Dodevski I, Babbitt PC. PMID: 20011109.
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    57. Glutathione transferases are structural and functional outliers in the thioredoxin fold. Biochemistry. 2009 Nov 24; 48(46):11108-16. Atkinson HJ, Babbitt PC. PMID: 19842715.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    58. The global cysteine peptidase landscape in parasites. Trends Parasitol. 2009 Dec; 25(12):573-81. Atkinson HJ, Babbitt PC, Sajid M. PMID: 19854678.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimals
    59. An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput Biol. 2009 Oct; 5(10):e1000541. Atkinson HJ, Babbitt PC. PMID: 19851441.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    60. A mapping of drug space from the viewpoint of small molecule metabolism. PLoS Comput Biol. 2009 Aug; 5(8):e1000474. Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt PC. PMID: 19701464.
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    61. 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. Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, Almo SC, Raushel FM. PMID: 19518059.
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    62. SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis. 2009 Jun 02; 3(6):e449. 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. PMID: 19488406.
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    63. Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric-8. Protein Sci. 2009 Jun; 18(6):1139-45. Figueroa M, Hinrichs MV, Bunster M, Babbitt P, Martinez-Oyanedel J, Olate J. PMID: 19472323.
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    64. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci. 2009 Jun; 18(6):1306-15. Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A. PMID: 19472362.
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    65. 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. 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. PMID: 19220063.
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    66. Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol. 2009 Feb; 13(1):10-8. Gerlt JA, Babbitt PC. PMID: 19237310.
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    67. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25. 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. PMID: 19219566.
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    68. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One. 2009; 4(2):e4345. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. PMID: 19190775.
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    69. Changes to NIH grant system may backfire. Science. 2008 Nov 21; 322(5905):1187-8. Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE. PMID: 19023064.
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    70. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov 12; 16(11):1668-77. Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. PMID: 19000819.
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    71. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry. 2008 Sep 23; 47(38):9944-54. Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA. PMID: 18754693.
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    72. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol. 2008 Aug 01; 4(8):e1000142. Chiang RA, Sali A, Babbitt PC. PMID: 18670595.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    73. Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways. Chem Biol. 2008 Jun; 15(6):607-18. Yoshikuni Y, Dietrich JA, Nowroozi FF, Babbitt PC, Keasling JD. PMID: 18559271.
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    74. 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. Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt PC, Almo SC, Raushel FM. PMID: 18171028.
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    75. Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans. Biochemistry. 2007 Nov 13; 46(45):12896-908. Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA. PMID: 17944491.
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    76. Differential use of protease families for invasion by schistosome cercariae. Biochimie. 2008 Feb; 90(2):345-58. 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. PMID: 17936488.
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    77. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One. 2007 Jul 18; 2(7):e617. 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. PMID: 17637833.
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    78. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 01; 23(17):2345-7. Morris JH, Huang CC, Babbitt PC, Ferrin TE. PMID: 17623706.
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    79. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug; 3(8):486-91. Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. PMID: 17603539.
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    80. Evolution of function in the "two dinucleotide binding domains" flavoproteins. PLoS Comput Biol. 2007 Jul; 3(7):e121. Ojha S, Meng EC, Babbitt PC. PMID: 17658942.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    81. 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. Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM. PMID: 17567048.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    82. Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry. 2007 Jun 12; 46(23):6688-95. Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. PMID: 17503785.
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    83. Mechanisms of protein evolution and their application to protein engineering. Adv Enzymol Relat Areas Mol Biol. 2007; 75:193-239, xii-xiii. Glasner ME, Gerlt JA, Babbitt PC. PMID: 17124868.
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    84. Comparison of methods for genomic localization of gene trap sequences. BMC Genomics. 2006 Sep 18; 7:236. Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC. PMID: 16982004.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    85. Evolution of enzyme superfamilies. Curr Opin Chem Biol. 2006 Oct; 10(5):492-7. Glasner ME, Gerlt JA, Babbitt PC. PMID: 16935022.
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    86. 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. Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. PMID: 16740275.
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    87. Using the Structure-function Linkage Database to characterize functional domains in enzymes. Curr Protoc Bioinformatics. 2006 Mar; Chapter 2:Unit 2.10. Brown S, Babbitt P. PMID: 18428763.
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    88. 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. Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA. PMID: 16489742.
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    89. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry. 2006 Feb 28; 45(8):2545-55. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. PMID: 16489747.
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    90. A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol. 2006; 7(1):R8. Brown SD, Gerlt JA, Seffernick JL, Babbitt PC. PMID: 16507141.
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    91. Automated discovery of 3D motifs for protein function annotation. Bioinformatics. 2006 Mar 15; 22(6):723-30. Polacco BJ, Babbitt PC. PMID: 16410325.
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    92. 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. 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. PMID: 16381950.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    93. Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys. 2005 Jan 01; 433(1):59-70. Gerlt JA, Babbitt PC, Rayment I. PMID: 15581566.
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    94. Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Pac Symp Biocomput. 2005; 319-21. Babbitt PC, Bourne PE, Mooney SD. PMID: 15759637.
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    95. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput. 2005; 358-69. Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC. PMID: 15759641.
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    96. 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. Copley SD, Novak WR, Babbitt PC. PMID: 15518547.
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    97. Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase. Biochemistry. 2004 Nov 02; 43(43):13766-74. Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC. PMID: 15504039.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    98. Superfamily active site templates. Proteins. 2004 Jun 01; 55(4):962-76. Meng EC, Polacco BJ, Babbitt PC. PMID: 15146493.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    99. Intersect: identification and visualization of overlaps in database search results. Bioinformatics. 2003 Oct 12; 19(15):1997-9. Pegg SC, Novak WR, Babbitt PC. PMID: 14555634.
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    100. 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. Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA. PMID: 12859183.
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    101. Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol. 2003 Apr; 7(2):230-7. Babbitt PC. PMID: 12714057.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    102. 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. McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, Kenyon GL. PMID: 12670968.
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    103. A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes. AAPS PharmSci. 2003; 5(1):E1. Brown S, Chang JL, Sadée W, Babbitt PC. PMID: 12713273.
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    104. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res. 2003 Jan 01; 31(1):278-81. 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. PMID: 12520002.
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    105. The Structure Superposition Database. Nucleic Acids Res. 2003 Jan 01; 31(1):505-10. Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. PMID: 12520064.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    106. 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. Lahiri SD, Wang PF, Babbitt PC, McLeish MJ, Kenyon GL, Allen KN. PMID: 12437342.
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    107. Expression of Torpedo californica creatine kinase in Escherichia coli and purification from inclusion bodies. Protein Expr Purif. 2002 Oct; 26(1):89-95. Wang PF, Novak WR, Cantwell JS, Babbitt PC, McLeish MJ, Kenyon GL. PMID: 12356475.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    108. 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. Wise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I. PMID: 11900527.
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    109. 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. Babbitt PC. PMID: 10984526.
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    110. 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. Wood TD, Chen LH, White CB, Babbitt PC, Kenyon GL, McLafferty FW.
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