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Papers authored by Babbitt PC

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The global cysteine peptidase landscape in parasites.

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Atkinson HJ, Babbitt PC, and Sajid M

Trends in parasitology 25(12):573-81, 2009 Dec - Who cited this? | PubMed ID: 19854678 | Fulltext

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

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Schnoes AM, Brown SD, Dodevski I, and Babbitt PC

PLoS computational biology 5(12):e1000605, 2009 Dec - Who cited this? | PubMed ID: 20011109 | Fulltext

Glutathione transferases are structural and functional outliers in the thioredoxin fold.

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Atkinson HJ and Babbitt PC

Biochemistry 48(46):11108-16, 2009 Nov 24 - Who cited this? | PubMed ID: 19842715 | Fulltext

An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations.

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Atkinson HJ and Babbitt PC

PLoS computational biology 5(10):e1000541, 2009 Oct - Who cited this? | PubMed ID: 19851441 | Fulltext

A mapping of drug space from the viewpoint of small molecule metabolism.

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Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, and Babbitt PC

PLoS computational biology 5(8):e1000474, 2009 Aug - Who cited this? | PubMed ID: 19701464 | Fulltext

Annotating Enzymes of Uncertain Function: The Deacylation of d-Amino Acids by Members of the Amidohydrolase Superfamily (,).

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Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, Almo SC, and Raushel FM

Biochemistry 48(27):6469-81, 2009 Jul 14 - Who cited this? | PubMed ID: 19518059 | Fulltext

Evolutionary constraints on structural similarity in orthologs and paralogs.

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Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, and Sali A

Protein science : a publication of the Protein Society 18(6):1306-15, 2009 Jun - Who cited this? | PubMed ID: 19472362 | Fulltext

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.

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Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM,

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Journal of structural and functional genomics 10(2):107-25, 2009 Apr - Who cited this? | PubMed ID: 19219566 | Fulltext

Evolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms in Two Families of cis,cis-Muconate Lactonizing Enzymes.

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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, and Gerlt JA

Biochemistry 48(11):2569-70, 2009 Mar 24 - Who cited this? | PubMed ID: 19292440 | Fulltext

Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.

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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, and Gerlt JA

Biochemistry 48(7):1445-53, 2009 Feb 24 - Who cited this? | PubMed ID: 19220063 | Fulltext

Enzyme (re)design: lessons from natural evolution and computation.

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Gerlt JA and Babbitt PC

Current opinion in chemical biology 13(1):10-8, 2009 Feb - Who cited this? | PubMed ID: 19237310 | Fulltext

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

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Atkinson HJ, Morris JH, Ferrin TE, and Babbitt PC

PLoS ONE 4(2):e4345, 2009 - Who cited this? | PubMed ID: 19190775 | Fulltext

SmCL3, a Gastrodermal Cysteine Protease of the Human Blood Fluke Schistosoma mansoni.

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Dvorák J, Mashiyama ST, Sajid M, Braschi S, Delcroix M, Schneider EL, McKerrow WH, Bahgat M, Hansell E, Babbitt PC, Craik CS, McKerrow JH, and Caffrey CR

PLoS neglected tropical diseases 3(6):e449, 2009 - Who cited this? | PubMed ID: 19488406 | Fulltext

Changes to NIH grant system may backfire.

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Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, and Bourne PE

Science (New York, N.Y.) 322(5905):1187-8, 2008 Nov 21 - Who cited this? | PubMed ID: 19023064 | Fulltext

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.

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Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, and Jacobson MP

Structure (London, England : 1993) 16(11):1668-77, 2008 Nov - Who cited this? | PubMed ID: 19000819 | Fulltext

Evolution of Enzymatic Activities in the Enolase Superfamily: l-Rhamnonate Dehydratase.

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Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, and Gerlt JA

Biochemistry, 2008 Aug 29 - Who cited this? | PubMed ID: 18754693 | Fulltext

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

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Chiang RA, Sali A, and Babbitt PC

PLoS computational biology 4(8), 2008 Aug - Who cited this? | PubMed ID: 18670595 | Fulltext

Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways.

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Yoshikuni Y, Dietrich JA, Nowroozi FF, Babbitt PC, and Keasling JD

Chemistry & biology 15(6):607-18, 2008 Jun - Who cited this? | PubMed ID: 18559271 | Fulltext

Differential use of protease families for invasion by schistosome cercariae.

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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, and McKerrow JH

Biochimie 90(2):345-58, 2008 Feb - Who cited this? | PubMed ID: 17936488 | Fulltext

At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate.

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Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt PC, Almo SC, and Raushel FM

Biochemistry 47(4):1194, 2008 Jan 29 - Who cited this? | PubMed ID: 18171028 | Fulltext

Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.

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Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, and Gerlt JA

Biochemistry 46(45):12896-908, 2007 Nov 13 - Who cited this? | PubMed ID: 17944491 | Fulltext

structureViz: linking Cytoscape and UCSF Chimera.

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Morris JH, Huang CC, Babbitt PC, and Ferrin TE

Bioinformatics (Oxford, England) 23(17):2345, 2007 Sep 1 - Who cited this? | PubMed ID: 17623706 | Fulltext

Prediction and assignment of function for a divergent N-succinyl amino acid racemase.

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Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, and Gerlt JA

Nature chemical biology 3(8):486-91, 2007 Aug - Who cited this? | PubMed ID: 17603539 | Fulltext

Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.

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Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, and Raushel FM

Biochemistry 46(27):7953-62, 2007 Jul 10 - Who cited this? | PubMed ID: 17567048 | Fulltext

Evolution of function in the "two dinucleotide binding domains" flavoproteins.

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Ojha S, Meng EC, and Babbitt PC

PLoS computational biology 3(7), 2007 Jul - Who cited this? | PubMed ID: 17658942 | Fulltext

Stability for function trade-offs in the enolase superfamily "catalytic module".

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Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, and Babbitt PC

Biochemistry 46(23):6688-95, 2007 Jun 12 - Who cited this? | PubMed ID: 17503785 | Fulltext

Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.

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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, and Conklin BR

PLoS ONE 2(7), 2007 - Who cited this? | PubMed ID: 17637833 | Fulltext

Mechanisms of protein evolution and their application to protein engineering.

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Glasner ME, Gerlt JA, and Babbitt PC

Advances in enzymology and related areas of molecular biology 75:193-239, xii-xiii, 2007 - Who cited this? | PubMed ID: 17124868 | Fulltext

Evolution of enzyme superfamilies.

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Glasner ME, Gerlt JA, and Babbitt PC

Current opinion in chemical biology 10(5):492-7, 2006 Oct - Who cited this? | PubMed ID: 16935022 | Fulltext

Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.

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Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, and Babbitt PC

Journal of molecular biology 360(1):228-50, 2006 Jun 30 - Who cited this? | PubMed ID: 16740275 | Fulltext

Automated discovery of 3D motifs for protein function annotation.

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Polacco BJ and Babbitt PC

Bioinformatics (Oxford, England) 22(6):723, 2006 Mar 15 - Who cited this? | PubMed ID: 16410325 | Fulltext

D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily.

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Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, and Gerlt JA

Biochemistry 45(8):2493-503, 2006 Feb 28 - Who cited this? | PubMed ID: 16489742 | Fulltext

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.

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Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, and Babbitt PC

Biochemistry 45(8):2545-55, 2006 Feb 28 - Who cited this? | PubMed ID: 16489747 | Fulltext

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.

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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,

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Nucleic acids research 34(Database issue):D642-8, 2006 Jan 1 - Who cited this? | PubMed ID: 16381950 | Fulltext

A gold standard set of mechanistically diverse enzyme superfamilies.

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Brown SD, Gerlt JA, Seffernick JL, and Babbitt PC

Genome biology 7(1):R8, 2006 - Who cited this? | PubMed ID: 16507141 | Fulltext

Comparison of methods for genomic localization of gene trap sequences.

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Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, and Babbitt PC

BMC genomics 7:236, 2006 - Who cited this? | PubMed ID: 16982004 | Fulltext

Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity.

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Gerlt JA, Babbitt PC, and Rayment I

Archives of biochemistry and biophysics 433(1):59-70, 2005 Jan 1 - Who cited this? | PubMed ID: 15581566 | Fulltext

Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure.

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Babbitt PC, Bourne PE, and Mooney SD

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:319-21, 2005 - Who cited this? | PubMed ID: 15759637 | Fulltext

Representing structure-function relationships in mechanistically diverse enzyme superfamilies.

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Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, and Babbitt PC

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:358-69, 2005 - Who cited this? | PubMed ID: 15759641 | Fulltext

Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor.

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Copley SD, Novak WR, and Babbitt PC

Biochemistry 43(44):13981-95, 2004 Nov 9 - Who cited this? | PubMed ID: 15518547 | Fulltext

Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase.

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Novak WR, Wang PF, McLeish MJ, Kenyon GL, and Babbitt PC

Biochemistry 43(43):13766-74, 2004 Nov 2 - Who cited this? | PubMed ID: 15504039 | Fulltext

Superfamily active site templates.

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Meng EC, Polacco BJ, and Babbitt PC

Proteins 55(4):962-76, 2004 Jun 1 - Who cited this? | PubMed ID: 15146493 | Fulltext

Intersect: identification and visualization of overlaps in database search results.

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Pegg SC, Novak WR, and Babbitt PC

Bioinformatics (Oxford, England) 19(15):1997-9, 2003 Oct 12 - Who cited this? | PubMed ID: 14555634 | Fulltext

Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily.

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Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, and Gerlt JA

Biochemistry 42(28):8387-93, 2003 Jul 22 - Who cited this? | PubMed ID: 12859183 | Fulltext

Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.

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McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, and Kenyon GL

Journal of bacteriology 185(8):2451-6, 2003 Apr - Who cited this? | PubMed ID: 12670968 | Fulltext

Definitions of enzyme function for the structural genomics era.

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Babbitt PC

Current opinion in chemical biology 7(2):230-7, 2003 Apr - Who cited this? | PubMed ID: 12714057 | Fulltext

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.

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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, and Ferrin TE

Nucleic acids research 31(1):278-81, 2003 Jan 1 - Who cited this? | PubMed ID: 12520002 | Fulltext

The Structure Superposition Database.

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Chiang RA, Meng EC, Huang CC, Ferrin TE, and Babbitt PC

Nucleic acids research 31(1):505-10, 2003 Jan 1 - Who cited this? | PubMed ID: 12520064 | Fulltext

A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes.

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Brown S, Chang JL, Sadée W, and Babbitt PC

AAPS pharmSci 5(1):E1, 2003 - Who cited this? | PubMed ID: 12713273 | Fulltext

The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg(2+)-NO(3)(-)-creatine transition-state analogue complex.

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Lahiri SD, Wang PF, Babbitt PC, McLeish MJ, Kenyon GL, and Allen KN

Biochemistry 41(47):13861-7, 2002 Nov 26 - Who cited this? | PubMed ID: 12437342 | Fulltext

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