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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 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. 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:    Fields:    
    2. 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
    3. 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:    
    4. 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: 19     Fields:    Translation:HumansAnimalsCells
    5. 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
    6. 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:    
    7. 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:    
    8. 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: 227     Fields:    Translation:HumansAnimalsCells
    9. 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: 7     Fields:    Translation:Cells
    10. 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: 19     Fields:    Translation:Cells
    11. 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: 1     Fields:    Translation:Cells
    12. 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: 7     Fields:    Translation:HumansAnimalsCells
    13. 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: 5     Fields:    Translation:Cells
    14. 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: 19     Fields:    
    15. 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:    
    16. 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: 5     Fields:    Translation:Cells
    17. 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
    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. 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:    
    20. 3D Motifs. From Protein Structure to Function with Bioinformatics. 2017 Jan 1; 361-392. Jerome P. Nilmeier, Elaine C. Meng, Benjamin J. Polacco, Patricia C. Babbitt. .
      View in: Publisher Site   Mentions:
    21. 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: 380     Fields:    Translation:HumansCells
    22. 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
    23. 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: 10     Fields:    Translation:AnimalsCells
    24. 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: 70     Fields:    Translation:Humans
    25. 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
    26. 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
    27. 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: 4     Fields:    Translation:Humans
    28. 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:    
    29. 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: 6     Fields:    Translation:Cells
    30. Enzyme ‘Social’ Networks: Tracking Sequence / Function Relationships to Elucidate Determinants of Enzyme Specificity and Mechanism. The FASEB Journal. 2015 Apr 1; 29. Eyal Akiva, Shoshana Brown, Gemma Holliday, Patricia Babbitt. .
      View in: Publisher Site   Mentions:
    31. [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: 18     Fields:    Translation:Cells
    32. 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: 5     Fields:    Translation:HumansAnimals
    33. 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
    34. 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: 8     Fields:    
    35. 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: 19     Fields:    Translation:HumansCells
    36. 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: 34     Fields:    Translation:Cells
    37. 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
    38. 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
    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. PMID: 24756107.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    40. The Nucleophilic Attack Six-Bladed ß-Propeller (N6P) Superfamily. Protein Families. 2013 Dec 13; 125-158. Michael A. Hicks, Alan E. Barber, Patricia C. Babbitt. .
      View in: Publisher Site   Mentions:
    41. 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: 79     Fields:    
    42. 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: 41     Fields:    Translation:Cells
    43. 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
    44. 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: 38     Fields:    Translation:HumansAnimals
    45. 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: 33     Fields:    Translation:Cells
    46. The nature of sequence and structure divergence in the Haloalkanoate Dehalogenase SuperFamily (HADSF). The FASEB Journal. 2013 Apr 1; 27:797.2-797.2. Chetanya Pandya, Shoshana D Brown, Debra Dunaway-Mariano, Patricia C Babbitt, Yu Xia, Karen N Allen. .
      View in: Publisher Site   Mentions:
    47. 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:    
    48. 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: 253     Fields:    Translation:HumansAnimals
    49. 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
    50. 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
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    66. 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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    81. 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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    82. 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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    134. New functions from old scaffolds: how nature reengineers enzymes for new functions. Adv Protein Chem. 2000; 55:1-28. Babbitt PC, Gerlt JA. PMID: 11050931.
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    135. Shotgun: getting more from sequence similarity searches. Bioinformatics. 1999 Sep; 15(9):729-40. Pegg SC, Babbitt PC. PMID: 10498773.
      View in: PubMed   Mentions: 9     Fields:    
    136. 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. PMID: 10387005.
      View in: PubMed   Mentions: 17     Fields:    Translation:CellsPHPublic Health
    137. 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. PMID: 10194342.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    138. 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. PMID: 9772161.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    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. PMID: 9772162.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    140. 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. PMID: 9818186.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    141. 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. PMID: 9724714.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    142. 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. PMID: 9649311.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    143. 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. PMID: 9388188.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCells
    144. 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. PMID: 9195965.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    145. 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. PMID: 8987982.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansCells
    146. 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. PMID: 8931562.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    147. 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.
    148. 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. PMID: 7768890.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    149. 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. PMID: 7855594.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    150. S-MANDEL ATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA: CONSTRUCTION OF A SOLUBLE CHIMERIC MUTANT OF A MEMBRANE-BOUND ENZYME. . 1994 Dec 31; 621-624. Bharati Mitra, John A. Gerlt, Patricia C. Babbitt, George L. Kenyon, Diane Joseph, Gregory A. Petsko. .
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    151. 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. PMID: 7765837.
      View in: PubMed   Mentions: 16     Fields:    Translation:CellsPHPublic Health
    152. 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. PMID: 8241149.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    153. 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. PMID: 1390752.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    154. 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. PMID: 1449598.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    155. 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. PMID: 1351742.
      View in: PubMed   Mentions: 50     Fields:    Translation:AnimalsCells
    156. ChemInform Abstract: Novel Enzymic Hydrolytic Dehalogenation of a Chlorinated Aromatic. ChemInform. 1991 Dec 17; 22(50):no-no. J. D. SCHOLTEN, K.-H. CHANG, P. C. BABBITT, H. CHAREST, M. SYLVESTRE, D. DUNAWAY-MARIANO. .
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    157. Active Creatine Kinase Refolded from Inclusion Bodies in Escherichia coli. Protein Refolding. 1991 Jul 30; 470:153-168. Patricia C. Babbitt, Brian L. West, Douglas D. Buechter, Lorenzo H. Chen, Irwin D. Kuntz, George L. Kenyon. .
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    158. 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. PMID: 1853203.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    159. 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. PMID: 2050699.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    160. Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs. Biochemistry. 1990 Dec 04; 29(48):10757-65. Pocalyko DJ, Carroll LJ, Martin BM, Babbitt PC, Dunaway-Mariano D. PMID: 2176881.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    161. Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli. Biochemistry. 1990 Oct 23; 29(42):9856-62. Tsou AY, Ransom SC, Gerlt JA, Buechter DD, Babbitt PC, Kenyon GL. PMID: 2271624.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    162. Removal of a proteolytic activity associated with aggregates formed from expression of creatine kinase in Escherichia coli leads to improved recovery of active enzyme. Biotechnology (N Y). 1990 Oct; 8(10):945-9. Babbitt PC, West BL, Buechter DD, Kuntz ID, Kenyon GL. PMID: 1370005.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    163. Adenosine 5'-[.alpha.,.beta.-imido]triphosphate, a substrate for T7 RNA polymerase and rabbit muscle creatine kinase [Erratum to document cited in CA109(1):6886j]. Journal of the American Chemical Society. 1988 Nov 1; 110(24):8267-8267. Qi Feng. Ma, Patricia C. Babbitt, George L. Kenyon. .
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    164. ChemInform Abstract: Adenosine 5'-(a,ß-Imido)triphosphate, a Substrate for T7 RNA Polymerase and Rabbit Muscle Creatine Kinase. ChemInform. 1988 Sep 27; 19(39). Q. MA, P. C. BABBITT, G. L. KENYON. .
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    165. Adenosine 5'-[.alpha.,.beta.-imido]triphosphate, a substrate for T7 RNA polymerase and rabbit muscle creatine kinase. Journal of the American Chemical Society. 1988 Jun 1; 110(12):4060-4061. Qi Feng. Ma, Patricia C. Babbitt, George L. Kenyon. .
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    166. Comparisons of creatine kinase primary structures. The Protein Journal. 1986 Feb 1; 5(1):1-14. Patricia C. Babbitt, George L. Kenyon, Irwin D. Kuntz, Fred E. Cohen, John D. Baxter, Pamela A. Benfield, Jean D. Buskin, William A. Gilbert, Steven D. Hauschka, Johann P. Hossle, Charles P. Ordahl, Mark L. Pearson, Jean-C. Perriard, Lulu A. Pickering, Scott D. Putney, Brian L. West, Robert A. Ziven. .
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    167. Creatine kinase protein sequence encoded by a cDNA made from Torpedo californica electric organ mRNA. Proc Natl Acad Sci U S A. 1984 Nov; 81(22):7007-11. West BL, Babbitt PC, Mendez B, Baxter JD. PMID: 6594677.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    168. Fingerprinting and characterization of carboxylic acids in in-situ oil shale retort and process waters by capillary column gas chromatography-mass spectrometry. Fuel. 1982 Mar 1; 61(3):227-231. Richard H. Fish, Amos S. Newton, Patricia C. Babbitt. .
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