Linking Sequence and Structure
with Function

California Institute for Quantitative Biosciences (QB3)
University of California San Francisco
1700 4th Street, 5th Floor
San Francisco, CA 94158


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Evaluating functional annotations of enzymes using the Gene Ontology.
Holliday GL, Davidson R, Akiva E, Babbitt PC.
Methods Mol Biol. 2017;1446:111-132.

DASP3: identification of protein sequences belonging to functionally relevant groups.
Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS.
BMC Bioinformatics. 2016 Nov 11;17(1):458.

Molecular diversity of terpene synthases in the liverwort Marchantia polymorpha.
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.
Plant Cell. 2016 Oct;28(10):2632-2650.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, et al.
Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

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Evolutionary reprograming of protein-protein interaction specificity.
Akiva E, Babbitt PC.
Cell. 2015 Oct 22;163(3):535-7. doi: 10.1016/j.cell.2015.10.010. Epub 2015 Oct 22.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.
Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, Fetrow JS.
Protein Sci. 2015 Sep;24(9):1423-39. doi: 10.1002/pro.2724. Epub 2015 Aug 18.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
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 Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.
Database (Oxford). 2015 Jul 11;2015:bav063. doi: 10.1093/database/bav063. eCollection 2015.

Key challenges for the creation and maintenance of specialist protein resources.
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.
Proteins. 2015 Jun;83(6):1005-13. doi: 10.1002/prot.24803. Epub 2015 Apr 22.

Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.
Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC.
Nucleic Acids Res. 2015 May 19;43(9):4602-13. doi: 10.1093/nar/gkv206. Epub 2015 Apr 8.

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.
Database (Oxford). 2015 May 9;2015. pii: bav043. Print 2015.

[FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis.
Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, Peters JW, Shepard EM, Broderick JB.
Biochemistry. 2015 Mar 10;54(9):1807-18. doi: 10.1021/bi501205e. Epub 2015 Mar 2.

Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.
London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK.
Biochemistry. 2015 Jan 20;54(2):528-37. doi: 10.1021/bi501140k. Epub 2015 Jan 5.

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New insights about enzyme evolution from large scale studies of sequence and structure relationships.
Brown SD, Babbitt PC.
J Biol Chem. 2014 Oct 31;289(44):30221-8. doi: 10.1074/jbc.R114.569350. Epub 2014 Sep 10.

Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach.
Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP.
PLoS Comput Biol. 2014 Oct 9;10(10):e1003874. doi: 10.1371/journal.pcbi.1003874.

Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.
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.
eLife. 2014 Jun 30;3. doi: 10.7554/eLife.03275.

Prediction of substrates for glutathione transferases by covalent docking.
Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A.
J Chem Inf Model. 2014 Jun 23;54(6):1687-99. doi: 10.1021/ci5001554. Epub 2014 May 16.

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.
Casey AK, Hicks MA, Johnson JL, Babbitt PC, Frantom PA.
Biochemistry. 2014 May 13;53(18):2915-25. doi: 10.1021/bi500246z. Epub 2014 Apr 22.

Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere.
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.
PLoS Biol. 2014 Apr 22;12(4):e1001843. doi: 10.1371/journal.pbio.1001843. eCollection 2014 Apr.

The Structure-Function Linkage Database.
Akiva E, Brown S, Almonacid DE, Barber AE 2nd, 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.
Nucleic Acids Res. 2014 Jan 1;42(1):D521-30. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23.

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Discovery of new enzymes and metabolic pathways by using structure and genome context.
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.
Nature. 2013 Oct 31;502(7473):698-702. doi: 10.1038/nature12576.

Consequences of domain insertion on sequence-structure divergence in a superfold.
Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN.
Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3381-7. Epub 2013 Aug 19.

Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.
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.
Nature. 2013 Jun 6;498(7452):123-6. Epub 2013 May 15.

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.
Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I.
PLoS Comput Biol. 2013 May;9(5):e1003063. Epub 2013 May 30.

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD.
Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1196-202. Epub 2013 Mar 14.

A large-scale evaluation of computational protein function prediction.
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.
Nat Methods. 2013 Mar;10(3):221-7. Epub 2013 Jan 27.

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A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets.
Mashiyama ST, Koupparis K, Caffrey CR, McKerrow JH, Babbitt PC.
PLoS Negl Trop Dis. 2012;6(12):e1942. Epub 2012 Dec 6.

Pythoscape: a framework for generation of large protein similarity networks.
Barber AE 2nd, Babbitt PC.
Bioinformatics. 2012 Nov 1;28(21):2845-6. Epub 2012 Sep 8.

Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis.
Crawford ED, Seaman JE, Barber AE 2nd, David DC, Babbitt PC, Burlingame AL, Wells JA.
Cell Death Differ. 2012 Dec;19(12):2040-8. Epub 2012 Aug 24.

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
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, Almo SC, Gerlt JA, Jacobson MP.
Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5.

Divergent evolution in enolase superfamily: strategies for assigning functions.
Gerlt JA, Babbitt PC, Jacobson MP, Almo SC.
J Biol Chem. 2012 Jan 2;287(1):29-34. Epub 2011 Nov 8.

Inference of functional properties from large-scale analysis of enzyme superfamilies.
Brown SD, Babbitt PC.
J Biol Chem. 2012 Jan 2;287(1):35-42. Epub 2011 Nov 8.

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The Enzyme Function Initiative.
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.
Biochemistry. 2011 Nov 22;50(46):9950-62. Epub 2011 Oct 26.

The evolution of function in strictosidine synthase-like proteins.
Hicks MA, Barber AE 2nd, Giddings LA, Caldwell J, O'Connor SE, Babbitt PC.
Proteins. 2011 Nov;79(11):3082-98. Epub 2011 Sep 21.

Toward mechanistic classification of enzyme functions.
Almonacid DE, Babbitt PC.
Curr Opin Chem Biol. 2011 Jun;15(3):435-42. Epub 2011 Apr 12.

Mutations in PNKD causing paroxysmal dyskinesia alters protein cleavage and stability.
Shen Y, Lee HY, Rawson J, Ojha S, Babbitt P, Fu YH, Ptácek LJ.
Hum Mol Genet. 2011 Jun 15;20(12):2322-32. Epub 2011 Apr 12.

Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies.
Meng EC, Babbitt PC.
Curr Opin Struct Biol. 2011 Jun;21(3):391-7. Epub 2011 Apr 1.

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
Apeltsin L, Morris JH, Babbitt PC, Ferrin TE.
Bioinformatics. 2011 Feb 1;27(3):326-33. Epub 2010 Nov 29.

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Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.
Almonacid DE, Yera ER, Mitchell JB, Babbitt PC.
PLoS Comput Biol. 2010 Mar 12;6(3):e1000700.

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Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
Schnoes AM, Brown SD, Dodevski I, Babbitt PC.
PLoS Comput Biol. 2009 Dec;5(12):e1000605. Epub 2009 Dec 11.

The global cysteine peptidase landscape in parasites.
Atkinson HJ, Babbitt PC, Sajid M.
Trends Parasitol. 2009 Dec;25(12):573-81. Epub 2009 Oct 24.

An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations.
Atkinson HJ, Babbitt PC.
PLoS Comput Biol. 2009 Oct;5(10):e1000541. Epub 2009 Oct 23.

Glutathione transferases are structural and functional outliers in the thioredoxin fold.
Atkinson HJ, Babbitt PC.
Biochemistry. 2009 Nov 24;48(46):11108-16.

A mapping of drug space from the viewpoint of small molecule metabolism.
Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt PC.
PLoS Comput Biol. 2009 Aug;5(8):e1000474. Epub 2009 Aug 21.

Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily.
Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, Almo SC, Raushel FM.
Biochemistry. 2009 Jul 14;48(27):6469-81.

SmCL3, a Gastrodermal Cysteine Protease of the Human Blood Fluke Schistosoma mansoni.
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.
PLoS Negl Trop Dis. 2009 Jun 2;3(6):e449.

Evolutionary constraints on structural similarity in orthologs and paralogs.
Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A.
Protein Sci. 2009 Jun;18(6):1306-15.

Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric-8.
Figueroa M, Hinrichs MV, Bunster M, Babbitt P, Martinez-Oyanedel J, Olate J.
Protein Sci. 2009 Jun;18(6):1139-45.

Enzyme (re)design: lessons from natural evolution and computation.
Gerlt JA, Babbitt PC.
Curr Opin Chem Biol. 2009 Feb;13(1):10-8. Epub 2009 Feb 23.

Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.
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.
Biochemistry. 2009 Feb 24;48(7):1445-53. Erratum in: Biochemistry. 2009 Mar 24;48(11):2569-70.

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
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, Jacobson MP, Babbitt PC, Sali A.
J Struct Funct Genomics. 2009 Apr;10(2):107-25. Epub 2009 Feb 14.

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.
Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC.
PLoS One. 2009;4(2):e4345. Epub 2009 Feb 3.

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Changes to NIH grant system may backfire.
Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE.
Science. (2008) Nov 21;322(5905):1187-1188.

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP.
Structure. (2008) Nov 12;16(11):1668-1677.

Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.
Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA.
Biochemistry. (2008) Sep 23;47(38):9944-9954.

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
Chiang RA, Sali A, Babbitt PC.
PLoS Comput Biol. (2008) Aug 1;4(8):e1000142.

Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways.
Yoshikuni Y, Dietrich JA, Nowroozi FF, Babbitt PC, Keasling JD.
Chem Biol. (2008) Jun;15(6):607-618.

At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate.
Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt PC, Almo SC, Raushel FM.
Biochemistry. (2008) Jan 29;47(4):1194-1206.

Differential use of protease families for invasion by schistosome cercariae.
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.
Biochimie. (2008) Feb;90(2):345-358.

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Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.
Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA.
Biochemistry. (2007) Nov 13;46(45):12896-12908.

Evolution of function in the “two dinucleotide binding domains” flavoproteins.
Ojha S, Meng EC, Babbitt PC.
PLoS Comput Biol. (2007) Jul 20;3(7):e121.

Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.
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.
PLoS ONE. (2007) Jul 18;2(7):e617.

structureViz: linking Cytoscape and UCSF Chimera.
Morris JH, Huang CC, Babbitt PC, Ferrin TE.
Bioinformatics. (2007) Sep 1;23(17):2345-2347.

Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA.
Nat Chem Biol. (2007) Aug;3(8):486-491.

Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.
Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM.
Biochemistry. (2007) Jul 10;46(27):7953-7962.

Stability for function trade-offs in the enolase superfamily "catalytic module".
Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC.
Biochemistry. (2007) Jun 12;46(23):6688-6695.

Mechanisms of protein evolution and their application to protein engineering.
Glasner ME, Gerlt JA, Babbitt PC.
Adv Enzymol Relat Areas Mol Biol. (2007) 75:193-239, xii-xiii.

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Comparison of methods for genomic localization of gene trap sequences.
Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC.
BMC Genomics. (2006) Sep 18;7:236.

Evolution of enzyme superfamilies.
Glasner ME, Gerlt JA, Babbitt PC.
Curr Opin Chem Biol. (2006) Oct;10(5):492-497.

Evolution of structure and function in the o-succinylbenzoatesynthase/N-acylamino acid racemase family of the enolase superfamily.
Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA,Babbitt PC.
J Mol Biol. (2006) Jun 30;360(1):228-250.

Automated discovery of 3D motifs for protein function annotation.
Polacco BJ, Babbitt PC.
Bioinformatics. (2006) Mar 15;22(6):723-730.

Using the Structure-function Linkage Database to characterize functional domains in enzymes.
Brown S, Babbitt P.
Curr Protoc Bioinformatics. (2006) Mar;Chapter 2:Unit 2.10.

Leveraging enzyme structure-function relationships for functional inference andexperimental design: the structure-function linkage database.
Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, HuangCC, Ferrin TE, Babbitt PC.
Biochemistry. (2006) Feb 28;45(8):2545-55.

D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships tomembers of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily.
Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA.
Biochemistry. (2006) Feb 28;45(8):2493-2503.

A gold standard set of mechanistically diverse enzyme superfamilies.
Brown SD, Gerlt JA, Seffernick JL, Babbitt PC.
Genome Biol. (2006) 7(1):R8.

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, JohnsSJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC,Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG,Babbitt PC, Ferrin TE.
Nucleic Acids Res. (2006) Jan 1;34(Database issue):D642-8.

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Representing structure-function relationships in mechanistically diverse enzymesuperfamilies.
Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC.
Pac Symp Biocomput. (2005) 358-69.

Introduction to informatics approaches in structural genomics: modeling andrepresentation of function from macromolecular structure.
Babbitt PC, Bourne PE, Mooney SD.
Pac Symp Biocomput. (2005) 319-21.

Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity.
Gerlt JA, Babbitt PC, Rayment I.
Arch Biochem Biophys. (2005) Jan 1;433(1):59-70.

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Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor.
Copley SD, Novak WR, Babbitt PC.
Biochemistry. (2004) Nov 9;43(44):13981-95.

Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase.
Novak WR, Wang PF, McLeish MJ, Kenyon GL, Babbitt PC.
Biochemistry. (2004) Nov 2;43(43):13766-74.

Superfamily active site templates.
Meng EC, Polacco BJ, Babbitt PC.
Proteins. (2004) Jun 1;55(4):962-76.

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Intersect: identification and visualization of overlaps in database search results.
Pegg SC, Novak WR, Babbitt PC.
Bioinformatics. (2003) Oct 12;19(15):1997-9.

Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily.
Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA.
Biochemistry. (2003) Jul 22;42(28):8387-93.

Definitions of enzyme function for the structural genomics era.
Babbitt PC.
Curr Opin Chem Biol. (2003) Apr;7(2):230-7.

Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.
McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, Kenyon GL.
J Bacteriol. (2003) Apr;185(8):2451-6.

The Structure Superposition Database.
Chiang, R.A, Meng, E.C., Huang, C.C., Thomas E. Ferrin, T.E., & Babbitt, P.C.
Nuc. Acids Res. 31 (2003) 505-510.

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.
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.
Nucleic Acids Res. (2003) Jan 1;31(1):278-81.

A Semiautomated Approach to Gene Discovery Through Expressed Sequence Tag Data Mining: Discovery of New Human Transporter Genes.
Brown S, Chang JL, Sadee W, Babbitt PC.
AAPS PharmSci; (2003) - 5(1) article 1

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Homologous (/) 8-Barrel Enzymes That Catalyze Unrelated Reactions: Orotidine 5'-Monophosphate Decarboxylase and 3-Keto-L-Gulonate 6-Phosphate Decarboxylase.
Eric Wise, Wen Shan Yew, Patricia C. Babbitt, John A. Gerlt, and Ivan Rayment.
Biochem. 41 (2002) 3861-3869.

The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg(2+)-NO(3)(-)-creatine transition-state analogue complex.
Lahiri SD, Wang PF, Babbitt PC, McLeish MJ, Kenyon GL, Allen KN.
Biochemistry. (2002) Nov 26;41(47):13861-7.

Expression of Torpedo californica creatine kinase in Escherichia coli and purification from inclusion bodies.
Wang PF, Novak WR, Cantwell JS, Babbitt PC, McLeish MJ, Kenyon GL.
Protein Expr Purif. (2002) Oct;26(1):89-95.

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Barrels in pieces?
John A. Gerlt and Patricia C. Babbitt.
Nature Structural Biology 8 (2001) 5-7.

Mutagenesis of two acidic active site residues in human muscle creatine kinase: Implications for the catalytic mechanism.
John S. Cantwell, Walter R. Novak, Pan-Fen Wang, Michael J. McLeish, George L. Kenyon, and Patricia C. Babbitt.
Biochem. 40 (2001) 3056-3061.

Functional assignment of the 20S Proteasome from T. brucei using mass spectrometry and new bioinformatics approaches.
Lan Huang, Richard J. Jacob, Scott C.-H. Pegg, Michael A. Baldwin, C.C. Wang, A.L. Burlingame, Patricia C. Babbitt.
Jour. Biol. Chem. 276 (2001) 28327-28339.

Divergent Evolution of Enzymatic Function: Mechanistically Diverse Superfamilies and Functionally Distinct Suprafamilies.
Gerlt, J.A. & Babbitt, P.C.
Ann. Rev. of Biochem. 70 (2001) 209-246.

ViewFEATURE: Integrated FEATURE analysis and visualization.
D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, & Teri E. Klein.
Pacific Symposium on Biocomputing Vol. 6, Edited by Russell B. Altman, Teri E. Klein, A. Keith Dunker, and Lawrence Hunter. World Interscience, Singapore, (2001).

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A comparative study of human muscle and brain creatine kinases expressed in E. coli.
Lorenzo H. Chen, Camille B. White, Patricia C. Babbitt, Michael J. McLeish & George L. Kenyon
J. Prot. Chem. 19 (2000) 59-66.

Re-engineering the glutathione S-transferase scaffold: A rational design strategy pays off.
Patricia C. Babbitt. (Commentary)
Proc. Natl. Acad. Sci. USA 97 (2000) 10298-10300.

Can sequence determine function?
John A. Gerlt and Patricia C. Babbitt.
Genome Biology 1 (2000) 0005.1-10.

Integrated Tools for Structural and Sequence Alignment and Analysis.
Conrad C. Huang, Walter R. Novak, Patricia C. Babbitt, Andrew I. Jewett, Thomas E. Ferrin, and Teri E. Klein.
Pacific Symposium on Biocomputing Vol. 5, Edited by Russell B. Altman, Teri E. Klein, A. Keith Dunker, and Lawrence Hunter. World Interscience, Singapore, (2000).

Protein Superfamily Building Methods Comparison.
Kunbin Qu, JunZhu, Scott C.-H. Pegg , Patricia Babbitt.
Currents in Computational Molecular Biology, pp. 139-140. Universal Academy Press, Inc. (2000).

New Functions from Old Scaffolds: How NatureRe-engineers Enzymes for New Functions.
Patricia C. Babbitt & John A. Gerlt.
Evolutionary Approaches to Protein Design, series: Advances in Protein Chemistry, Vol. 55. Edited by Frances H. Arnold, Academic Press, San Diego, CA, (2000) 1-28.

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Evidence that pcpA Encodes 2,6-Dichlorohydroquinone Dioxygenase, the Ring Cleavage Enzyme Required for Pentachlorophenol Degradation in Sphingomonas chlorophenolica Strain ATCC 39723.
Ling Xu, Katheryn Resing, Sherry L. Lawson, Patricia C. Babbitt, and Shelley D. Copley.
Biochem. 38 (1999) 7659-7669.

Unexpected divergence of function and sequence in orthologous enzymes: "N-acylamino acid racemase" from Amycolaptosis is o-succinylbenzoate synthase.
David R.J. Palmer, James B. Garrett, R. Meganathan, Patricia C. Babbitt, and John A. Gerlt.
Biochem. 38 (1999) 4252-4258.

Shotgun: getting more from sequence similarity searches.
Scott C-H. Pegg and Patricia C. Babbitt.
Bioinformatics 15 (1999) 729-740.

Structure-Based Sequence Alignment of Mandelate Racemase and Muconate Lactonizing Enzyme: Superposition on Reality.
Miriam S. Hasson, Patricia C. Babbitt, Dagmar Ringe, Gregory A. Petsko and George L. Kenyon.
Enzymatic Mechanisms, pp. 308-316. Edited by P.A. Frey and D. B. Northrup. IOS Press, (1999).

Insights into the mechanism of catalysis by P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis.
Angela S. Baker, Michael J. Ciocci, William W. Metcalf, Jaebong Kim, Patricia C. Babbitt, Barry L. Wanner, Brian M. Martin, and Debra Dunaway-Mariano.
Biochem., 37 (1998), 9305-9315.

Evolution of an enzyme active site: The structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.
Miriam S. Hasson, Ilme Schlichting, Javad Moulai, Kirk Taylor, William Barrett, George L. Kenyon, Patricia C. Babbitt, John A. Gerlt, Gregory A. Petsko, and Dagmar Ringe.
Proc. Natl. Acad. Sci. USA, 95 (1998), 10396-10401.

Evolution of enzymatic activities in the Enolase Superfamily: Characterization of the (D) Glucarate/Galactarate catabolic pathway in Escherichia coli.
Brian K. Hubbard, Marjan Koch, David R. J. Palmer, Patricia C. Babbitt, and John A. Gerlt.
Biochem., 37 (1998) 14369-14375.

Evolution of Enzymatic Activities in the Enolase Superfamily: Crystal Structure of (D) Glucarate Dehydratase from Pseudomonas putida.
Andrew M. Gulick, David R. J. Palmer, Patricia C. Babbitt, John A. Gerlt, and Ivan Rayment.
Biochem., 37 (1998) 14358-14368.

Mechanistically diverse enzyme superfamilies: The importance of chemistry in the evolution of catalysis.
John A. Gerlt and Patricia C. Babbitt.
Cur. Op. Chem. Biol., 2 (1998) 607-612.

Superfamily analysis: Understanding protein function from structure and sequence.
Patricia C. Babbitt and Teri E. Klein.
Encyclopedia Comp Chem, Edited by P.v.R. Schleyer. Wiley Interscience, (1998).

Cloning and functional characterization of a rat renal organic cation transporter isoform.
Lei Zhang, Mark J. Dresser, Joanne K. Chun, Patricia C. Babbitt, and Kathleen M. Giacomini.
J. Biol. Chem. 272 (1997) 16548-16554 .

Understanding enzyme superfamilies: Chemistry as the fundamental determinant in the evolution of new catalytic activities.
Patricia C. Babbitt and John A. Gerlt.
J. Biol. review 272 (1997) 30591-30594.

Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione s-transferase superfamily: Oxidative damage or mutagenesis of cys13 converts tetrachlorohydroquinone dehalogenase into a gluthathione S-transferase.
Darla L. McCarthy, Sandra Navarrete, W. Scott Willett, Patricia C. Babbitt, and Shelley D. Copley.
Biochem. 35, (1996) 14634-14642.

The enolase superfamily: A general strategy for enzyme-catalyzed abstraction of the ?-protons of carboxylic acids.
Patricia C. Babbitt, Miriam S. Hasson, Joseph E. Wedekind, David R. Palmer, George H. Reed, Ivan Rayment, Dagmar Ringe, George L. Kenyon, and John A. Gerlt.
Biochem. 35, (1996) 16489-16501.

A functionally diverse superfamily that abstracts the alpha-protons of carboxylic acids.
Patricia C. Babbitt, Gregory T. Mrachko, Miriam Sarah Hasson, Gjalt W. Huisman, Roberto Kolter, Dagmar Ringe, Gregory A. Petsko, George L. Kenyon, and John A. Gerlt.
Science 267 (1995) 1159-1161.

A novel activity of OmpT: Proteolysis under extreme denaturing conditions.
Camille Bodley White, Qun Chen, George L. Kenyon, and Patricia C. Babbitt.
J. Biol. Chem. 270 (1995) 12990-12994.

Sequence verification of human creatine kinase (43KD) isozymes by high resolution tandem mass spectrometry.
Troy D. Wood, Lorenzo H. Chen, Camille B. White, Patricia C. Babbitt, George L. Kenyon, and F.W. McLafferty.
Proc. Natl. Acad. Sci. USA 92 (1995) 11451-5.

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