Patricia Babbitt, PhD

Title(s)Professor Emeritus, Bioengineering
SchoolSchool of Pharmacy
AddressLocation Required
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 T32GM067547Jul 1, 2003 - Jun 30, 2023
    Role: Co-Principal Investigator
    Laying the Foundation of Genomic Enzymology
    NIH R01GM060595Mar 1, 2000 - Jul 31, 2019
    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. Kinetic and Structural Analysis of Two Linkers in the Tautomerase Superfamily: Analysis and Implications. Biochemistry. 2021 Jun 08; 60(22):1776-1786. Baas BJ, Medellin BP, LeVieux JA, Erwin K, Lancaster EB, Johnson WH, Kaoud TS, Moreno RY, de Ruijter M, Babbitt PC, Zhang YJ, Whitman CP. PMID: 34019384.
      View in: PubMed   Mentions:    Fields:    
    2. Parallel molecular mechanisms for enzyme temperature adaptation. Science. 2021 03 05; 371(6533). Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. PMID: 33674467.
      View in: PubMed   Mentions: 3     Fields:    
    3. Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer. Biochemistry. 2020 04 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:    Translation:Cells
    4. A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database (Oxford). 2020 01 01; 2020. Holliday GL, Brown SD, Mischel D, Polacco BJ, Babbitt PC. PMID: 32449511.
      View in: PubMed   Mentions: 1     Fields:    
    5. 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: 48     Fields:    Translation:HumansAnimalsCells
    6. 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
    7. 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: 5     Fields:    
    8. 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: 1     Fields:    
    9. 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: 438     Fields:    Translation:HumansAnimalsCells
    10. 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: 13     Fields:    Translation:Cells
    11. 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: 30     Fields:    Translation:Cells
    12. 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: 3     Fields:    Translation:Cells
    13. 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: 12     Fields:    Translation:HumansAnimalsCells
    14. 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: 6     Fields:    Translation:Cells
    15. 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: 32     Fields:    
    16. 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:    
    17. 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: 8     Fields:    Translation:Cells
    18. 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
    19. 3D Motifs. From Protein Structure to Function with Bioinformatics. 2017 Jan 1; 361-392. Nilmeier NJ, Meng ME, Polacco PB, Babbitt BP. .
      View in: Publisher Site   Mentions:
    20. 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: 4     Fields:    Translation:HumansAnimals
    21. 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:    
    22. 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: 479     Fields:    Translation:HumansCells
    23. 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
    24. 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, 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; PMCID: PMC5134972.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    25. 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, 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; PMCID: PMC5015320.
      View in: PubMed   Mentions: 100     Fields:    Translation:Humans
    26. Evolutionary reprograming of protein-protein interaction specificity. Cell. 2015 Oct 22; 163(3):535-7. Akiva E, Babbitt PC, Akiva E, Babbitt PC. PMID: 26496596.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    27. 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, Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, Fetrow JS. PMID: 26073648; PMCID: PMC4570537.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    28. 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, 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; PMCID: PMC4499208.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    29. 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, 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; PMCID: PMC4446195.
      View in: PubMed   Mentions: 6     Fields:    
    30. 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, Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC. PMID: 25855808; PMCID: PMC4482062.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    31. Enzyme ‘Social’ Networks: Tracking Sequence / Function Relationships to Elucidate Determinants of Enzyme Specificity and Mechanism. The FASEB Journal. 2015 Apr 1; 29. Akiva AE, Brown BS, Holliday HG, Babbitt BP. .
      View in: Publisher Site   Mentions:
    32. [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, Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, Peters JW, Shepard EM, Broderick JB. PMID: 25654171; PMCID: PMC4839199.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    33. 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, 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; PMCID: PMC4303301.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimals
    34. 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, Brown S, Babbitt P. PMID: 25501940; PMCID: PMC4349220.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    35. 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, Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. PMID: 25299649; PMCID: PMC4191879.
      View in: PubMed   Mentions: 8     Fields:    
    36. New insights about enzyme evolution from large scale studies of sequence and structure relationships. J Biol Chem. 2014 Oct 31; 289(44):30221-30228. Brown SD, Babbitt PC, Brown SD, Babbitt PC. PMID: 25210038; PMCID: PMC4215206.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    37. 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, 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; PMCID: PMC4113996.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    38. 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, 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; PMCID: PMC4068255.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    39. 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, 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; PMCID: PMC3995644.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    40. Mechanistic and bioinformatic investigation of a conserved active site helix in α-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. Biochemistry. 2014 May 13; 53(18):2915-25. Casey AK, Hicks MA, Johnson JL, Babbitt PC, Frantom PA, Casey AK, Hicks MA, Johnson JL, Babbitt PC, Frantom PA. PMID: 24720347; PMCID: PMC4025573.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
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    91. 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, Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. PMID: 17503785.
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    92. 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, Glasner ME, Gerlt JA, Babbitt PC. PMID: 17124868.
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    93. 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, Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC. PMID: 16982004; PMCID: PMC1617135.
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    94. Evolution of enzyme superfamilies. Curr Opin Chem Biol. 2006 Oct; 10(5):492-7. Glasner ME, Gerlt JA, Babbitt PC, Glasner ME, Gerlt JA, Babbitt PC. PMID: 16935022.
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    95. 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, Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. PMID: 16740275.
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    96. 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, Brown S, Babbitt P. PMID: 18428763.
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    97. Improving Comparative Structure Modeling through the Use of Multiple Templates. The FASEB Journal. 2006 Mar 1; 20(4):a491-a491. Peterson PM, Babbitt BP, Sali SA. .
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    98. Evaluating function in uncharacterized enzymes. The FASEB Journal. 2006 Mar 1; 20(5):a904-a904. Schnoes SA, Dodevski DI, Babbitt BP. .
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    99. The Structure-Function Linkage Database. The FASEB Journal. 2006 Mar 1; 20(5):a899-a899. Brown BS, Pegg PS, Ojha OS, Huang HC, Ferrin FT, Babbitt BP. .
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    100. Investigating the properties of catalytic module residues in the enolase superfamily: Effects on thermostability. The FASEB Journal. 2006 Mar 1; 20(5):a901-a901. Nagatani NR, Babbitt BP. .
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    101. Evolutionary relationships in the glutathione reductase superfamily. The FASEB Journal. 2006 Mar 1; 20(5):a905-a905. Ojha OS, Meng ME, Babbitt BP. .
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    102. Evolution of structure and function in the o-succinylbenzoate synthase family. The FASEB Journal. 2006 Mar 1; 20(5):a905-a905. Glasner GM, Fayazmanesh FN, Chiang CR, Jacobson JM, Gerlt GJ, Babbitt BP. .
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    103. Characterizing the structure-function relationship in the thioredoxin fold class. The FASEB Journal. 2006 Mar 1; 20(5):a907-a907. Atkinson AH, Babbitt BP. .
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    104. 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, Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA. PMID: 16489742.
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    105. 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, 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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    106. A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol. 2006; 7(1):R8. Brown SD, Gerlt JA, Seffernick JL, Babbitt PC, Brown SD, Gerlt JA, Seffernick JL, Babbitt PC. PMID: 16507141; PMCID: PMC1431709.
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    107. Automated discovery of 3D motifs for protein function annotation. Bioinformatics. 2006 Mar 15; 22(6):723-30. Polacco BJ, Babbitt PC, Polacco BJ, Babbitt PC. PMID: 16410325.
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    108. 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, 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; PMCID: PMC1347459.
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    109. 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, Gerlt JA, Babbitt PC, Rayment I. PMID: 15581566.
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    110. 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, Babbitt PC, Bourne PE, Mooney SD. PMID: 15759637.
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    111. 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, Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC. PMID: 15759641.
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    112. 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, Copley SD, Novak WR, Babbitt PC. PMID: 15518547.
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    113. 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, Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC. PMID: 15504039.
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    114. Superfamily active site templates. Proteins. 2004 Jun 01; 55(4):962-76. Meng EC, Polacco BJ, Babbitt PC, Meng EC, Polacco BJ, Babbitt PC. PMID: 15146493.
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    115. Intersect: identification and visualization of overlaps in database search results. Bioinformatics. 2003 Oct 12; 19(15):1997-9. Pegg SC, Novak WR, Babbitt PC, Pegg SC, Novak WR, Babbitt PC. PMID: 14555634.
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    116. 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, Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA. PMID: 12859183.
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    117. Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol. 2003 Apr; 7(2):230-7. Babbitt PC, Babbitt PC. PMID: 12714057.
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    118. 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, McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, Kenyon GL. PMID: 12670968; PMCID: PMC152609.
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    119. 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, Brown S, Chang JL, Sadée W, Babbitt PC. PMID: 12713273; PMCID: PMC2751469.
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    120. 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, 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; PMCID: PMC165511.
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    121. The Structure Superposition Database. Nucleic Acids Res. 2003 Jan 01; 31(1):505-10. Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC, Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. PMID: 12520064; PMCID: PMC165574.
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    122. 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, Lahiri SD, Wang PF, Babbitt PC, McLeish MJ, Kenyon GL, Allen KN. PMID: 12437342.
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    123. 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, Wang PF, Novak WR, Cantwell JS, Babbitt PC, McLeish MJ, Kenyon GL. PMID: 12356475.
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    124. Superfamily Analysis: Understanding Protein Function from Structure and Sequence. Encyclopedia of Computational Chemistry. 2002 Apr 15. Babbitt BP, Klein KT. .
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    125. 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, Wise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I. PMID: 11900527.
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    126. 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. Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AL, Babbitt PC, Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AL, Babbitt PC. PMID: 11309374.
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    127. 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. Cantwell JS, Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC, Cantwell JS, Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC. PMID: 11258919.
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    128. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem. 2001; 70:209-46. Gerlt JA, Babbitt PC, Gerlt JA, Babbitt PC. PMID: 11395407.
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    129. Barrels in pieces? Nat Struct Biol. 2001 Jan; 8(1):5-7. Gerlt JA, Babbitt PC, Gerlt JA, Babbitt PC. PMID: 11135656.
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    130. ViewFeature: integrated feature analysis and visualization. Pac Symp Biocomput. 2001; 240-50. Banatao DR, Huang CC, Babbitt PC, Altman RB, Klein TE, Banatao DR, Huang CC, Babbitt PC, Altman RB, Klein TE. PMID: 11262944.
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    131. Can sequence determine function? Genome Biol. 2000; 1(5):REVIEWS0005. Gerlt JA, Babbitt PC, Gerlt JA, Babbitt PC. PMID: 11178260; PMCID: PMC138884.
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    132. 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, Babbitt PC. PMID: 10984526; PMCID: PMC34038.
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    133. A comparative study of human muscle and brain creatine kinases expressed in Escherichia coli. J Protein Chem. 2000 Jan; 19(1):59-66. Chen LH, White CB, Babbitt PC, McLeish MJ, Kenyon GL, Chen LH, White CB, Babbitt PC, McLeish MJ, Kenyon GL. PMID: 10882173.
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    134. Integrated tools for structural and sequence alignment and analysis. Pac Symp Biocomput. 2000; 230-41. Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE, Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE. PMID: 10902172.
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    135. New functions from old scaffolds: how nature reengineers enzymes for new functions. Adv Protein Chem. 2000; 55:1-28. Babbitt PC, Gerlt JA, Babbitt PC, Gerlt JA. PMID: 11050931.
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    136. Shotgun: getting more from sequence similarity searches. Bioinformatics. 1999 Sep; 15(9):729-40. Pegg SC, Babbitt PC, Pegg SC, Babbitt PC. PMID: 10498773.
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    137. 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. Xu L, Resing K, Lawson SL, Babbitt PC, Copley SD, Xu L, Resing K, Lawson SL, Babbitt PC, Copley SD. PMID: 10387005.
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    138. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry. 1999 Apr 06; 38(14):4252-8. Palmer DR, Garrett JB, Sharma V, Meganathan R, Babbitt PC, Gerlt JA, Palmer DR, Garrett JB, Sharma V, Meganathan R, Babbitt PC, Gerlt JA. PMID: 10194342.
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    139. 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. Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA, Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA. PMID: 9772162.
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    140. 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. Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I, Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I. PMID: 9772161.
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    141. Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis. Curr Opin Chem Biol. 1998 Oct; 2(5):607-12. Gerlt JA, Babbitt PC, Gerlt JA, Babbitt PC. PMID: 9818186.
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    142. 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 01; 95(18):10396-401. Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt PC, Gerlt JA, Petsko GA, Ringe D, Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt PC, Gerlt JA, Petsko GA, Ringe D. PMID: 9724714; PMCID: PMC27905.
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    143. 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. Baker AS, Ciocci MJ, Metcalf WW, Kim J, Babbitt PC, Wanner BL, Martin BM, Dunaway-Mariano D, Baker AS, Ciocci MJ, Metcalf WW, Kim J, Babbitt PC, Wanner BL, Martin BM, Dunaway-Mariano D. PMID: 9649311.
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    144. Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities. J Biol Chem. 1997 Dec 05; 272(49):30591-4. Babbitt PC, Gerlt JA, Babbitt PC, Gerlt JA. PMID: 9388188.
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    145. Cloning and functional characterization of a rat renal organic cation transporter isoform (rOCT1A). J Biol Chem. 1997 Jun 27; 272(26):16548-54. Zhang L, Dresser MJ, Chun JK, Babbitt PC, Giacomini KM, Zhang L, Dresser MJ, Chun JK, Babbitt PC, Giacomini KM. PMID: 9195965.
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    146. 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. Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA, Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA. PMID: 8987982.
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    147. Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry. 1996 Nov 19; 35(46):14634-42. McCarthy DL, Navarrete S, Willett WS, Babbitt PC, Copley SD, McCarthy DL, Navarrete S, Willett WS, Babbitt PC, Copley SD. PMID: 8931562.
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    148. 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.
    149. A novel activity of OmpT. Proteolysis under extreme denaturing conditions. J Biol Chem. 1995 Jun 02; 270(22):12990-4. White CB, Chen Q, Kenyon GL, Babbitt PC, White CB, Chen Q, Kenyon GL, Babbitt PC. PMID: 7768890.
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    150. A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids. Science. 1995 Feb 24; 267(5201):1159-61. Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA, Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA. PMID: 7855594.
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    151. S-MANDEL ATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA: CONSTRUCTION OF A SOLUBLE CHIMERIC MUTANT OF A MEMBRANE-BOUND ENZYME. . 1994 Dec 31; 621-624. Mitra MB, Gerlt GJ, Babbitt BP, Kenyon KG, Joseph JD, Petsko PG. .
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    152. 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. Dunaway-Mariano D, Babbitt PC, Dunaway-Mariano D, Babbitt PC. PMID: 7765837.
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    153. 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 07; 32(48):12959-67. Mitra B, Gerlt JA, Babbitt PC, Koo CW, Kenyon GL, Joseph D, Petsko GA, Mitra B, Gerlt JA, Babbitt PC, Koo CW, Kenyon GL, Joseph D, Petsko GA. PMID: 8241149.
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    154. 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. Williams SE, Woolridge EM, Ransom SC, Landro JA, Babbitt PC, Kozarich JW, Williams SE, Woolridge EM, Ransom SC, Landro JA, Babbitt PC, Kozarich JW. PMID: 1390752.
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    155. 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. White KC, Babbitt PC, Buechter DD, Kenyon GL, White KC, Babbitt PC, Buechter DD, Kenyon GL. PMID: 1449598.
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    156. 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. Babbitt PC, Kenyon GL, Martin BM, Charest H, Slyvestre M, Scholten JD, Chang KH, Liang PH, Dunaway-Mariano D, Babbitt PC, Kenyon GL, Martin BM, Charest H, Slyvestre M, Scholten JD, Chang KH, Liang PH, Dunaway-Mariano D. PMID: 1351742.
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    157. ChemInform Abstract: Novel Enzymic Hydrolytic Dehalogenation of a Chlorinated Aromatic. ChemInform. 1991 Dec 17; 22(50):no-no. SCHOLTEN SJ, CHANG CK, BABBITT BP, CHAREST CH, SYLVESTRE SM, DUNAWAY-MARIANO DD. .
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    158. Active Creatine Kinase Refolded from Inclusion Bodies in Escherichia coli. Protein Refolding. 1991 Jul 30; 470:153-168. Babbitt BP, West WB, Buechter BD, Chen CL, Kuntz KI, Kenyon KG. .
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    159. Novel enzymic hydrolytic dehalogenation of a chlorinated aromatic. Science. 1991 Jul 12; 253(5016):182-5. Scholten JD, Chang KH, Babbitt PC, Charest H, Sylvestre M, Dunaway-Mariano D, Scholten JD, Chang KH, Babbitt PC, Charest H, Sylvestre M, Dunaway-Mariano D. PMID: 1853203.
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    160. 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. Chen LH, Babbitt PC, Vásquez JR, West BL, Kenyon GL, Chen LH, Babbitt PC, Vásquez JR, West BL, Kenyon GL. PMID: 2050699.
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