Patricia C. Babbitt - Publications

Biophysics University of California, San Francisco, San Francisco, CA 
Bioinformatics Biology, Biochemistry, General Biophysics

135 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 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. Kinetic and Structural Analysis of Two Linkers in the Tautomerase Superfamily: Analysis and Implications. Biochemistry. PMID 34019384 DOI: 10.1021/acs.biochem.1c00220  0.44
2021 Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science (New York, N.Y.). 371. PMID 33674467 DOI: 10.1126/science.aay2784  0.44
2020 Holliday GL, Brown SD, Mischel D, Polacco BJ, Babbitt PC. A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database : the Journal of Biological Databases and Curation. 2020. PMID 32449511 DOI: 10.1093/Database/Baaa034  1
2020 Medellin BP, Lancaster EB, Brown S, Rakhade S, Babbitt PC, Whitman CP, Zhang YJ. Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer. Biochemistry. PMID 32242662 DOI: 10.1021/Acs.Biochem.0C00211  0.88
2019 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, Dalkıran A, ... ... Babbitt PC, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8  0.36
2019 Baas BJ, Medellin BP, LeVieux J, de Ruijter M, Zhang YJ, Brown SD, Akiva E, Babbitt PC, Whitman CP. Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer. Biochemistry. PMID 31074977 DOI: 10.1021/Acs.Biochem.9B00303  0.84
2019 Copp JN, Anderson DW, Akiva E, Babbitt PC, Tokuriki N. Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions. Methods in Enzymology. 620: 315-347. PMID 31072492 DOI: 10.1016/Bs.Mie.2019.03.015  0.44
2018 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, et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Research. PMID 30398656 DOI: 10.1093/Nar/Gky1100  0.84
2018 Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods in Enzymology. 606: 1-71. PMID 30097089 DOI: 10.1016/Bs.Mie.2018.06.004  0.84
2018 Yunes JM, Babbitt PC. Effusion: Prediction of Protein Function from Sequence Similarity Networks. Bioinformatics (Oxford, England). PMID 30084920 DOI: 10.1093/Bioinformatics/Bty672  0.36
2018 Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry. PMID 30052428 DOI: 10.1021/Acs.Biochem.8B00473  0.44
2017 Davidson R, Baas BJ, Akiva E, Holliday GL, Polacco BJ, LeVieux JA, Pullara CR, Zhang YJ, Whitman CP, Babbitt PC. A global view of structure-function relationships in the tautomerase superfamily. The Journal of Biological Chemistry. PMID 29184004 DOI: 10.1074/Jbc.M117.815340  1
2017 LeVieux JA, Baas BJ, Kaoud TS, Davidson R, Babbitt PC, Zhang YJ, Whitman CP. Kinetic and structural characterization of a cis-3-Chloroacrylic acid dehalogenase homologue in Pseudomonas sp. UW4: A potential step between subgroups in the tautomerase superfamily. Archives of Biochemistry and Biophysics. PMID 29111295 DOI: 10.1016/J.Abb.2017.10.018  0.44
2017 Akiva E, Copp JN, Tokuriki N, Babbitt PC. Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078300 DOI: 10.1073/Pnas.1706849114  0.44
2017 Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database : the Journal of Biological Databases and Curation. 2017. PMID 28605775 DOI: 10.1093/database/bax045  0.84
2017 Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database : the Journal of Biological Databases and Curation. 2017. PMID 28365730 DOI: 10.1093/Database/Bax006  0.84
2017 Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. Plos Computational Biology. 13: e1005284. PMID 28187133 DOI: 10.1371/Journal.Pcbi.1005284  0.56
2017 Knutson ST, Westwood BM, Leuthaeuser JB, Turner B, Nguyendac D, Shea G, Kumar K, Hayden J, Harper A, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Science : a Publication of the Protein Society. PMID 28054422 DOI: 10.1002/Pro.3112  0.84
2017 Holliday GL, Davidson R, Akiva E, Babbitt PC. Evaluating Functional Annotations of Enzymes Using the Gene Ontology. Methods in Molecular Biology (Clifton, N.J.). 1446: 111-132. PMID 27812939 DOI: 10.1007/978-1-4939-3743-1_9  0.48
2016 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, et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Research. PMID 27899635 DOI: 10.1093/Nar/Gkw1107  0.48
2016 Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. DASP3: identification of protein sequences belonging to functionally relevant groups. Bmc Bioinformatics. 17: 458. PMID 27835946 DOI: 10.1186/S12859-016-1295-Z  0.56
2016 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, ... ... Babbitt PC, et al. Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha. The Plant Cell. PMID 27650333 DOI: 10.1105/Tpc.16.00062  0.84
2016 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, ... ... Babbitt PC, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  0.4
2015 Akiva E, Babbitt PC. Evolutionary reprograming of protein-protein interaction specificity. Cell. 163: 535-7. PMID 26496596 DOI: 10.1016/J.Cell.2015.10.010  0.44
2015 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, et al. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database : the Journal of Biological Databases and Curation. 2015: bav063. PMID 26284514 DOI: 10.1093/Database/Bav063  1
2015 Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC. Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification. Nucleic Acids Research. 43: 4602-13. PMID 25855808 DOI: 10.1093/Nar/Gkv206  1
2015 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, ... ... Babbitt PC, et al. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 83: 1005-13. PMID 25820941 DOI: 10.1002/Prot.24803  1
2015 Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, Peters JW, Shepard EM, Broderick JB. [FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. Biochemistry. 54: 1807-18. PMID 25654171 DOI: 10.1021/Bi501205E  1
2015 London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry. 54: 528-37. PMID 25513739 DOI: 10.1021/Bi501140K  1
2014 Brown S, Babbitt P. Using the structure-function linkage database to characterize functional domains in enzymes. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 48: 2.10.1-2.10.16. PMID 25501940 DOI: 10.1002/0471250953.Bi0210S48  0.88
2014 Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. Plos Computational Biology. 10: e1003874. PMID 25299649 DOI: 10.1371/Journal.Pcbi.1003874  1
2014 Brown SD, Babbitt PC. New insights about enzyme evolution from large scale studies of sequence and structure relationships. The Journal of Biological Chemistry. 289: 30221-8. PMID 25210038 DOI: 10.1074/Jbc.R114.569350  1
2014 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, et al. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 3. PMID 24980702 DOI: 10.7554/Elife.03275  1
2014 Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. Journal of Chemical Information and Modeling. 54: 1687-99. PMID 24802635 DOI: 10.1021/Ci5001554  1
2014 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, et al. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. Plos Biology. 12: e1001843. PMID 24756107 DOI: 10.1371/Journal.Pbio.1001843  1
2014 Casey AK, Hicks MA, Johnson JL, Babbitt PC, Frantom PA. 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. 53: 2915-25. PMID 24720347 DOI: 10.1021/Bi500246Z  1
2014 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, ... ... Babbitt PC, et al. The Structure-Function Linkage Database. Nucleic Acids Research. 42: D521-30. PMID 24271399 DOI: 10.1093/Nar/Gkt1130  1
2014 Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, Francisco BS, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, et al. Author response: Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks Elife. DOI: 10.7554/Elife.03275.025  0.88
2013 Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 502: 698-702. PMID 24056934 DOI: 10.1038/Nature12576  0.88
2013 Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. Consequences of domain insertion on sequence-structure divergence in a superfold. Proceedings of the National Academy of Sciences of the United States of America. 110: E3381-7. PMID 23959887 DOI: 10.1073/Pnas.1305519110  1
2013 Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I. Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space Plos Computational Biology. 9. PMID 23737737 DOI: 10.1371/Journal.Pcbi.1003063  1
2013 Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature. 498: 123-6. PMID 23676670 DOI: 10.1038/Nature12180  0.88
2013 Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD. Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proceedings of the National Academy of Sciences of the United States of America. 110: E1196-202. PMID 23493556 DOI: 10.1073/Pnas.1300632110  1
2012 Mashiyama ST, Koupparis K, Caffrey CR, McKerrow JH, Babbitt PC. A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. Plos Neglected Tropical Diseases. 6: e1942. PMID 23236535 DOI: 10.1371/Journal.Pntd.0001942  1
2012 Barber AE, Babbitt PC. Pythoscape: a framework for generation of large protein similarity networks. Bioinformatics (Oxford, England). 28: 2845-6. PMID 22962345 DOI: 10.1093/Bioinformatics/Bts532  1
2012 Crawford ED, Seaman JE, Barber AE, David DC, Babbitt PC, Burlingame AL, Wells JA. Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. Cell Death and Differentiation. 19: 2040-8. PMID 22918439 DOI: 10.1038/Cdd.2012.99  1
2012 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, et al. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proceedings of the National Academy of Sciences of the United States of America. 109: 4122-7. PMID 22392983 DOI: 10.1073/Pnas.1112081109  1
2012 Gerlt JA, Babbitt PC, Jacobson MP, Almo SC. Divergent evolution in enolase superfamily: strategies for assigning functions. The Journal of Biological Chemistry. 287: 29-34. PMID 22069326 DOI: 10.1074/Jbc.R111.240945  1
2012 Brown SD, Babbitt PC. Inference of functional properties from large-scale analysis of enzyme superfamilies. The Journal of Biological Chemistry. 287: 35-42. PMID 22069325 DOI: 10.1074/Jbc.R111.283408  0.84
2011 Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 50: 9950-62. PMID 21999478 DOI: 10.1021/Bi201312U  0.6
2011 Hicks MA, Barber AE, Giddings LA, Caldwell J, O'Connor SE, Babbitt PC. The evolution of function in strictosidine synthase-like proteins Proteins: Structure, Function and Bioinformatics. 79: 3082-3098. PMID 21948213 DOI: 10.1002/Prot.23135  1
2011 Shen Y, Lee HY, Rawson J, Ojha S, Babbitt P, Fu YH, Ptácek LJ. Mutations in PNKD causing paroxysmal dyskinesia alters protein cleavage and stability. Human Molecular Genetics. 20: 2322-32. PMID 21487022 DOI: 10.1093/Hmg/Ddr125  1
2011 Meng EC, Babbitt PC. Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies. Current Opinion in Structural Biology. 21: 391-7. PMID 21458983 DOI: 10.1016/J.Sbi.2011.03.007  1
2011 Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics (Oxford, England). 27: 326-33. PMID 21118823 DOI: 10.1093/Bioinformatics/Btq655  1
2010 Almonacid DE, Yera ER, Mitchell JB, Babbitt PC. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. Plos Computational Biology. 6: e1000700. PMID 20300652 DOI: 10.1371/Journal.Pcbi.1000700  1
2009 Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. Plos Computational Biology. 5: e1000605. PMID 20011109 DOI: 10.1371/Journal.Pcbi.1000605  1
2009 Atkinson HJ, Babbitt PC, Sajid M. The global cysteine peptidase landscape in parasites. Trends in Parasitology. 25: 573-81. PMID 19854678 DOI: 10.1016/J.Pt.2009.09.006  1
2009 Atkinson HJ, Babbitt PC. An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. Plos Computational Biology. 5: e1000541. PMID 19851441 DOI: 10.1371/Journal.Pcbi.1000541  1
2009 Atkinson HJ, Babbitt PC. Glutathione transferases are structural and functional outliers in the thioredoxin fold. Biochemistry. 48: 11108-16. PMID 19842715 DOI: 10.1021/Bi901180V  1
2009 Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt PC. A mapping of drug space from the viewpoint of small molecule metabolism. Plos Computational Biology. 5: e1000474. PMID 19701464 DOI: 10.1371/Journal.Pcbi.1000474  1
2009 Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, Almo SC, Raushel FM. Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily. Biochemistry. 48: 6469-81. PMID 19518059 DOI: 10.1021/Bi900661B  1
2009 Dvorák J, Mashiyama ST, Sajid M, Braschi S, Delcroix M, Schneider EL, McKerrow WH, Bahgat M, Hansell E, Babbitt PC, Craik CS, McKerrow JH, Caffrey CR. SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni. Plos Neglected Tropical Diseases. 3: e449. PMID 19488406 DOI: 10.1371/Journal.Pntd.0000449  1
2009 Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Science : a Publication of the Protein Society. 18: 1306-15. PMID 19472362 DOI: 10.1002/Pro.143  1
2009 Gerlt JA, Babbitt PC. Enzyme (re)design: lessons from natural evolution and computation Current Opinion in Chemical Biology. 13: 10-18. PMID 19237310 DOI: 10.1016/J.Cbpa.2009.01.014  1
2009 Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes. Biochemistry. 48: 1445-53. PMID 19220063 DOI: 10.1021/Bi802277H  1
2009 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, ... ... Babbitt PC, et al. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. Journal of Structural and Functional Genomics. 10: 107-25. PMID 19219566 DOI: 10.1007/S10969-008-9056-5  1
2009 Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. Plos One. 4: e4345. PMID 19190775 DOI: 10.1371/Journal.Pone.0004345  1
2008 Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE. Changes to NIH grant system may backfire Science. 322: 1187-1188. PMID 19023064 DOI: 10.1126/Science.322.5905.1187C  1
2008 Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure (London, England : 1993). 16: 1668-77. PMID 19000819 DOI: 10.1016/J.Str.2008.08.015  1
2008 Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase Biochemistry. 47: 9944-9954. PMID 18754693 DOI: 10.1021/Bi800914R  1
2008 Chiang RA, Sali A, Babbitt PC. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. Plos Computational Biology. 4: e1000142. PMID 18670595 DOI: 10.1371/Journal.Pcbi.1000142  1
2008 Yoshikuni Y, Dietrich JA, Nowroozi FF, Babbitt PC, Keasling JD. Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways. Chemistry & Biology. 15: 607-18. PMID 18559271 DOI: 10.1016/J.Chembiol.2008.05.006  1
2008 Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt PC, Almo SC, Raushel FM. At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate. Biochemistry. 47: 1194-206. PMID 18171028 DOI: 10.1021/Bi7017738  1
2008 Dvorák J, Mashiyama ST, Braschi S, Sajid M, Knudsen GM, Hansell E, Lim KC, Hsieh I, Bahgat M, Mackenzie B, Medzihradszky KF, Babbitt PC, Caffrey CR, McKerrow JH. Differential use of protease families for invasion by schistosome cercariae. Biochimie. 90: 345-58. PMID 17936488 DOI: 10.1016/J.Biochi.2007.08.013  1
2007 Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans. Biochemistry. 46: 12896-908. PMID 17944491 DOI: 10.1021/Bi701703W  1
2007 Ojha S, Meng EC, Babbitt PC. Evolution of function in the "two dinucleotide binding domains" flavoproteins. Plos Computational Biology. 3: e121. PMID 17658942 DOI: 10.1371/Journal.Pcbi.0030121  1
2007 Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. Plos One. 2: e617. PMID 17637833 DOI: 10.1371/Journal.Pone.0000617  1
2007 Morris JH, Huang CC, Babbitt PC, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics (Oxford, England). 23: 2345-7. PMID 17623706 DOI: 10.1093/Bioinformatics/Btm329  1
2007 Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nature Chemical Biology. 3: 486-91. PMID 17603539 DOI: 10.1038/Nchembio.2007.11  1
2007 Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM. Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase. Biochemistry. 46: 7953-62. PMID 17567048 DOI: 10.1021/Bi700544C  1
2007 Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry. 46: 6688-95. PMID 17503785 DOI: 10.1021/Bi700507D  1
2007 Glasner ME, Gerlt JA, Babbitt PC. Mechanisms of protein evolution and their application to protein engineering Advances in Enzymology and Related Areas of Molecular Biology. 75: 193-239. PMID 17124868 DOI: 10.1002/9780471224464.Ch3  1
2006 Brown S, Babbitt P. Using the Structure-function Linkage Database to characterize functional domains in enzymes. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 2.10. PMID 18428763 DOI: 10.1002/0471250953.bi0210s13  0.88
2006 Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC. Comparison of methods for genomic localization of gene trap sequences. Bmc Genomics. 7: 236. PMID 16982004 DOI: 10.1186/1471-2164-7-236  1
2006 Glasner ME, Gerlt JA, Babbitt PC. Evolution of enzyme superfamilies Current Opinion in Chemical Biology. 10: 492-497. PMID 16935022 DOI: 10.1016/J.Cbpa.2006.08.012  1
2006 Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. Evolution of Structure and Function in the o-Succinylbenzoate Synthase/N-Acylamino Acid Racemase Family of the Enolase Superfamily Journal of Molecular Biology. 360: 228-250. PMID 16740275 DOI: 10.1016/J.Jmb.2006.04.055  1
2006 Brown SD, Gerlt JA, Seffernick JL, Babbitt P. A gold standard set of mechanistically diverse enzyme superfamilies Genome Biology. 7. PMID 16507141 DOI: 10.1186/Gb-2006-7-1-R8  1
2006 Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry. 45: 2545-55. PMID 16489747 DOI: 10.1021/Bi052101L  1
2006 Akana J, Fedorov AA, Fedorov E, Novak WRP, Babbitt PC, Almo SC, Gerlt JA. D-ribulose 5-phosphate 3-epimerase: Functional and structural relationships to members of the ribulose-phosphate binding (β/α) 8-barrel superfamily Biochemistry. 45: 2493-2503. PMID 16489742 DOI: 10.1021/Bi052474M  1
2006 Polacco BJ, Babbitt PC. Automated discovery of 3D motifs for protein function annotation. Bioinformatics (Oxford, England). 22: 723-30. PMID 16410325 DOI: 10.1093/Bioinformatics/Btk038  1
2006 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, ... ... Babbitt PC, et al. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Research. 34: D642-8. PMID 16381950 DOI: 10.1093/Nar/Gkj097  1
2005 Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 358-69. PMID 15759641  1
2005 Babbitt PC, Bourne PE, Mooney SD. Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 319-21. PMID 15759637  1
2005 Gerlt JA, Babbitt PC, Rayment I. Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Archives of Biochemistry and Biophysics. 433: 59-70. PMID 15581566 DOI: 10.1016/J.Abb.2004.07.034  1
2004 Copley SD, Novak WR, Babbitt PC. Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry. 43: 13981-95. PMID 15518547 DOI: 10.1021/Bi048947R  0.56
2004 Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC. Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase. Biochemistry. 43: 13766-74. PMID 15504039 DOI: 10.1021/Bi049060Y  1
2004 Meng EC, Polacco BJ, Babbitt PC. Superfamily active site templates. Proteins. 55: 962-76. PMID 15146493 DOI: 10.1002/Prot.20099  1
2003 Pegg SC, Novak WR, Babbitt PC. Intersect: identification and visualization of overlaps in database search results. Bioinformatics (Oxford, England). 19: 1997-9. PMID 14555634 DOI: 10.1093/Bioinformatics/Btg256  0.56
2003 Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA. Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry. 42: 8387-93. PMID 12859183 DOI: 10.1021/Bi034769A  1
2003 Brown S, Chang JL, Sadée W, Babbitt PC. A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes. Aaps Pharmsci. 5: E1. PMID 12713273 DOI: 10.1208/Ps050101  0.88
2003 McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, Kenyon GL. Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633. Journal of Bacteriology. 185: 2451-6. PMID 12670968 DOI: 10.1128/Jb.185.8.2451-2456.2003  1
2003 Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. The Structure Superposition Database. Nucleic Acids Research. 31: 505-10. PMID 12520064 DOI: 10.1093/Nar/Gkg127  1
2003 Stryke D, Kawamoto M, Huang CC, Johns SJ, King LA, Harper CA, Meng EC, Lee RE, Yee A, L'Italien L, Chuang PT, Young SG, Skarnes WC, Babbitt PC, Ferrin TE. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Research. 31: 278-81. PMID 12520002 DOI: 10.1093/Nar/Gkg064  0.76
2002 Lahiri SD, Wang PF, Babbitt PC, McLeish MJ, Kenyon GL, Allen KN. The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg(2+)-NO(3)(-)-creatine transition-state analogue complex. Biochemistry. 41: 13861-7. PMID 12437342 DOI: 10.1021/Bi026655P  1
2002 Wang PF, Novak WR, Cantwell JS, Babbitt PC, McLeish MJ, Kenyon GL. Expression of Torpedo californica creatine kinase in Escherichia coli and purification from inclusion bodies. Protein Expression and Purification. 26: 89-95. PMID 12356475 DOI: 10.1016/S1046-5928(02)00512-0  1
2002 Wise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I. Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 41: 3861-9. PMID 11900527 DOI: 10.1021/Bi012174E  1
2001 Gerlt JA, Babbitt PC. Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies Annual Review of Biochemistry. 70: 209-246. PMID 11395407 DOI: 10.1146/Annurev.Biochem.70.1.209  1
2001 Cantwell JS, Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC. Mutagenesis of two acidic active site residues in human muscle creatine kinase: implications for the catalytic mechanism. Biochemistry. 40: 3056-61. PMID 11258919 DOI: 10.1021/Bi0020980  1
2001 Gerlt JA, Babbitt PC. Barrels in pieces? Nature Structural Biology. 8: 5-7. PMID 11135656 DOI: 10.1038/83048  1
2000 Gerlt JA, Babbitt PC. Can sequence determine function? Genome Biology. 1: REVIEWS0005. PMID 11178260 DOI: 10.1186/Gb-2000-1-5-Reviews0005  1
2000 Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE. Integrated tools for structural and sequence alignment and analysis. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 230-41. PMID 10902172  1
2000 Chen LH, White CB, Babbitt PC, McLeish MJ, Kenyon GL. A comparative study of human muscle and brain creatine kinases expressed in Escherichia coli. Journal of Protein Chemistry. 19: 59-66. PMID 10882173 DOI: 10.1023/A:1007047026691  1
1999 Xu L, Resing K, Lawson SL, Babbitt PC, Copley SD. Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723. Biochemistry. 38: 7659-69. PMID 10387005 DOI: 10.1021/Bi990103Y  1
1999 Palmer DR, Garrett JB, Sharma V, Meganathan R, Babbitt PC, Gerlt JA. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry. 38: 4252-8. PMID 10194342 DOI: 10.1021/Bi990140P  1
1998 Gerlt JA, Babbitt PC. Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis. Current Opinion in Chemical Biology. 2: 607-12. PMID 9818186 DOI: 10.1016/S1367-5931(98)80091-4  1
1998 Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry. 37: 14369-75. PMID 9772162 DOI: 10.1021/Bi981124F  1
1998 Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida. Biochemistry. 37: 14358-68. PMID 9772161 DOI: 10.1021/Bi981123N  1
1998 Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt PC, Gerlt JA, Petsko GA, Ringe D. Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase. Proceedings of the National Academy of Sciences of the United States of America. 95: 10396-401. PMID 9724714 DOI: 10.1073/Pnas.95.18.10396  1
1998 Baker AS, Ciocci MJ, Metcalf WW, Kim J, Babbitt PC, Wanner BL, Martin BM, Dunaway-Mariano D. Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis. Biochemistry. 37: 9305-15. PMID 9649311 DOI: 10.1021/Bi972677D  1
1997 Babbitt PC, Gerlt JA. Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities. The Journal of Biological Chemistry. 272: 30591-4. PMID 9388188 DOI: 10.1074/Jbc.272.49.30591  1
1997 Zhang L, Dresser MJ, Chun JK, Babbitt PC, Giacomini KM. Cloning and functional characterization of a rat renal organic cation transporter isoform (rOCT1A). The Journal of Biological Chemistry. 272: 16548-54. PMID 9195965 DOI: 10.1074/Jbc.272.26.16548  1
1996 Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA. The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry. 35: 16489-501. PMID 8987982 DOI: 10.1021/Bi9616413  1
1996 McCarthy DL, Navarrete S, Willett WS, Babbitt PC, Copley SD. Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry. 35: 14634-42. PMID 8931562 DOI: 10.1021/bi961730f  1
1995 Wood TD, Chen LH, White CB, Babbitt PC, Kenyon GL, McLafferty FW. Sequence verification of human creatine kinase (43 kDa) isozymes by high-resolution tandem mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 92: 11451-5. PMID 8524781 DOI: 10.1073/Pnas.92.25.11451  1
1995 Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA. A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids. Science (New York, N.Y.). 267: 1159-61. PMID 7855594 DOI: 10.1126/Science.7855594  1
1995 White CB, Chen Q, Kenyon GL, Babbitt PC. A novel activity of OmpT. Proteolysis under extreme denaturing conditions. The Journal of Biological Chemistry. 270: 12990-4. PMID 7768890 DOI: 10.1074/Jbc.270.22.12990  1
1994 Dunaway-Mariano D, Babbitt PC. On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway Biodegradation. 5: 259-276. PMID 7765837 DOI: 10.1007/Bf00696464  1
1992 White KC, Babbitt PC, Buechter DD, Kenyon GL. The principal islet of the Coho salmon (Oncorhyncus kisutch) contains the BB isoenzyme of creatine kinase. Journal of Protein Chemistry. 11: 489-94. PMID 1449598 DOI: 10.1007/Bf01025026  1
1992 Babbitt PC, Kenyon GL, Martin BM, Charest H, Slyvestre M, Scholten JD, Chang KH, Liang PH, Dunaway-Mariano D. Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases. Biochemistry. 31: 5594-604. PMID 1351742 DOI: 10.1021/Bi00139A024  1
1991 Scholten JD, Chang KH, Babbitt PC, Charest H, Sylvestre M, Dunaway-Mariano D. Novel enzymic hydrolytic dehalogenation of a chlorinated aromatic Science. 253: 182-185. PMID 1853203 DOI: 10.1126/Science.1853203  1
1990 Tsou AY, Ransom SC, Gerlt JA, Buechter DD, Babbitt PC, Kenyon GL. Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli. Biochemistry. 29: 9856-62. PMID 2271624 DOI: 10.1021/Bi00494A015  1
1990 Pocalyko DJ, Carroll LJ, Martin BM, Babbitt PC, Dunaway-Mariano D. Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: Sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs Biochemistry. 29: 10757-10765. PMID 2176881 DOI: 10.1021/Bi00500A006  1
1990 Babbitt PC, West BL, Buechter DD, Kuntz ID, Kenyon GL. Removal of a proteolytic activity associated with aggregates formed from expression of creatine kinase in Escherichia coli leads to improved recovery of active enzyme. Bio/Technology (Nature Publishing Company). 8: 945-9. PMID 1370005 DOI: 10.1038/Nbt1090-945  1
1986 Babbitt PC, Kenyon GL, Kuntz ID, Cohen FE, Baxter JD, Benfield PA, Buskin JD, Gilbert WA, Hauschka SD, Hossle JP, Ordahl CP, Pearson ML, Perriard JC, Pickering LA, Putney SD, et al. Comparisons of creatine kinase primary structures Journal of Protein Chemistry. 5: 1-14. DOI: 10.1007/Bf01025580  1
1984 West BL, Babbitt PC, Mendez B, Baxter JD. Creatine kinase protein sequence encoded by a cDNA made from Torpedo californica electric organ mRNA. Proceedings of the National Academy of Sciences of the United States of America. 81: 7007-11. PMID 6594677 DOI: 10.1073/Pnas.81.22.7007  0.72
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