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Shoshana Brown, Ph.D. - Publications

Affiliations: 
2005 University of California, San Francisco, San Francisco, CA 
Area:
Pharmaceutical Chemistry
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34 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
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  0.833
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  0.628
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  0.591
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  0.631
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  0.71
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  0.641
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  0.718
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  0.628
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, et al. Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha. The Plant Cell. PMID 27650333 DOI: 10.1105/Tpc.16.00062  0.593
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  0.659
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  0.648
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  0.721
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  0.704
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  0.751
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, et al. The Structure-Function Linkage Database. Nucleic Acids Research. 42: D521-30. PMID 24271399 DOI: 10.1093/Nar/Gkt1130  0.74
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  0.745
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  0.646
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  0.594
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  0.662
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  0.692
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  0.698
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  0.809
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  0.582
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  0.765
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, 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  0.791
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 ofcis,cis-Muconate Lactonizing Enzymes Biochemistry. 48: 2569-2570. DOI: 10.1021/Bi900265W  0.749
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  0.632
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  0.809
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  0.609
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  0.707
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  0.657
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  0.715
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  0.689
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  0.632
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