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Items: 1 to 50 of 139

1.

Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer.

Baas BJ, Medellin BP, LeVieux JA, de Ruijter M, Zhang YJ, Brown SD, Akiva E, Babbitt PC, Whitman CP.

Biochemistry. 2019 Jun 4;58(22):2617-2627. doi: 10.1021/acs.biochem.9b00303. Epub 2019 May 23.

PMID:
31074977
2.

Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions.

Copp JN, Anderson DW, Akiva E, Babbitt PC, Tokuriki N.

Methods Enzymol. 2019;620:315-347. doi: 10.1016/bs.mie.2019.03.015. Epub 2019 Apr 17.

PMID:
31072492
3.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360. doi: 10.1093/nar/gky1100.

4.

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain.

Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC.

Methods Enzymol. 2018;606:1-71. doi: 10.1016/bs.mie.2018.06.004. Epub 2018 Jul 24.

5.

Effusion: prediction of protein function from sequence similarity networks.

Yunes JM, Babbitt PC.

Bioinformatics. 2019 Feb 1;35(3):442-451. doi: 10.1093/bioinformatics/bty672.

6.

Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks.

Copp JN, Akiva E, Babbitt PC, Tokuriki N.

Biochemistry. 2018 Aug 7;57(31):4651-4662. doi: 10.1021/acs.biochem.8b00473. Epub 2018 Jul 27.

PMID:
30052428
7.

New computational approaches to understanding molecular protein function.

Fetrow JS, Babbitt PC.

PLoS Comput Biol. 2018 Apr 5;14(4):e1005756. doi: 10.1371/journal.pcbi.1005756. eCollection 2018 Apr. No abstract available.

8.

A global view of structure-function relationships in the tautomerase superfamily.

Davidson R, Baas BJ, Akiva E, Holliday GL, Polacco BJ, LeVieux JA, Pullara CR, Zhang YJ, Whitman CP, Babbitt PC.

J Biol Chem. 2018 Feb 16;293(7):2342-2357. doi: 10.1074/jbc.M117.815340. Epub 2017 Nov 28.

9.

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.

LeVieux JA, Baas BJ, Kaoud TS, Davidson R, Babbitt PC, Zhang YJ, Whitman CP.

Arch Biochem Biophys. 2017 Dec 15;636:50-56. doi: 10.1016/j.abb.2017.10.018. Epub 2017 Oct 27.

10.

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily.

Akiva E, Copp JN, Tokuriki N, Babbitt PC.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9549-E9558. doi: 10.1073/pnas.1706849114. Epub 2017 Oct 24.

11.

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax045. No abstract available.

12.

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax006. Erratum in: Database (Oxford). 2017 Jan 1;2017:null.

13.

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS.

PLoS Comput Biol. 2017 Feb 10;13(2):e1005284. doi: 10.1371/journal.pcbi.1005284. eCollection 2017 Feb.

14.

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS.

Protein Sci. 2017 Apr;26(4):677-699. doi: 10.1002/pro.3112. Epub 2017 Mar 8.

15.

InterPro in 2017-beyond protein family and domain annotations.

Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL.

Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29.

16.

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.

17.

Evaluating Functional Annotations of Enzymes Using the Gene Ontology.

Holliday GL, Davidson R, Akiva E, Babbitt PC.

Methods Mol Biol. 2017;1446:111-132.

18.

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. Epub 2016 Sep 20.

19.

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, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

20.

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.

21.

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.

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.

23.

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.

24.

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.

25.

[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.

26.

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.

27.

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. eCollection 2014 Oct.

28.

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. Review.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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;42(Database issue):D521-30. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23.

34.

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. Epub 2013 Sep 22.

35.

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. doi: 10.1073/pnas.1305519110. Epub 2013 Aug 19.

36.

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;9(5):e1003063. doi: 10.1371/journal.pcbi.1003063. Epub 2013 May 30.

37.

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. doi: 10.1038/nature12180. Epub 2013 May 15.

38.

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. doi: 10.1073/pnas.1300632110. Epub 2013 Mar 14.

39.

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. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

40.

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. doi: 10.1371/journal.pntd.0001942. Epub 2012 Dec 6.

41.

Pythoscape: a framework for generation of large protein similarity networks.

Barber AE 2nd, Babbitt PC.

Bioinformatics. 2012 Nov 1;28(21):2845-6. doi: 10.1093/bioinformatics/bts532. Epub 2012 Sep 8.

42.

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. doi: 10.1038/cdd.2012.99. Epub 2012 Aug 24.

43.

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. doi: 10.1073/pnas.1112081109. Epub 2012 Mar 5.

44.

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. doi: 10.1074/jbc.R111.240945. Epub 2011 Nov 8. Review.

45.

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. doi: 10.1074/jbc.R111.283408. Epub 2011 Nov 8. Review.

46.

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. doi: 10.1021/bi201312u. Epub 2011 Oct 26. Review.

47.

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. doi: 10.1002/prot.23135. Epub 2011 Sep 21.

48.

Toward mechanistic classification of enzyme functions.

Almonacid DE, Babbitt PC.

Curr Opin Chem Biol. 2011 Jun;15(3):435-42. doi: 10.1016/j.cbpa.2011.03.008. Epub 2011 Apr 12. Review.

49.

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. doi: 10.1016/j.sbi.2011.03.007. Epub 2011 Apr 1. Review.

50.

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. doi: 10.1093/bioinformatics/btq655. Epub 2010 Nov 29.

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