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Items: 1 to 50 of 83

1.

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.

2.

High rate of hypoglycemia in 6770 type 2 diabetes patients with comorbid dementia: A multicenter cohort study on 215,932 patients from the German/Austrian diabetes registry.

Prinz N, Stingl J, Dapp A, Denkinger MD, Fasching P, Jehle PM, Merger S, Mühldorfer S, Pieper U, Schuler A, Zeyfang A, Holl RW; DPV initiative.

Diabetes Res Clin Pract. 2016 Feb;112:73-81. doi: 10.1016/j.diabres.2015.10.026. Epub 2015 Oct 30.

PMID:
26563590
3.

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.

Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P.

PLoS Comput Biol. 2015 Aug 27;11(8):e1004362. doi: 10.1371/journal.pcbi.1004362. eCollection 2015 Aug.

4.

The loop2 insertion of type IX myosin acts as an electrostatic actin tether that permits processive movement.

Elfrink K, Liao W, Pieper U, Oeding SJ, Bähler M.

PLoS One. 2014 Jan 9;9(1):e84874. doi: 10.1371/journal.pone.0084874. eCollection 2014.

5.

ModBase, a database of annotated comparative protein structure models and associated resources.

Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D336-46. doi: 10.1093/nar/gkt1144. Epub 2013 Nov 23.

6.

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.

Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA.

PLoS Comput Biol. 2013;9(10):e1003253. doi: 10.1371/journal.pcbi.1003253. Epub 2013 Oct 3.

7.

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.

8.

A role for matrix metalloproteinases in regulating mammary stem cell function via the Wnt signaling pathway.

Kessenbrock K, Dijkgraaf GJ, Lawson DA, Littlepage LE, Shahi P, Pieper U, Werb Z.

Cell Stem Cell. 2013 Sep 5;13(3):300-13. doi: 10.1016/j.stem.2013.06.005. Epub 2013 Jul 18.

9.

Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.

Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout MP, Almo SC.

Structure. 2013 Apr 2;21(4):560-71. doi: 10.1016/j.str.2013.02.005. Epub 2013 Mar 14.

10.

Coordinating the impact of structural genomics on the human α-helical transmembrane proteome.

Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, Rees DC, Stokes DL, Stowell MH, Wiener MC, Rost B, Stroud RM, Stevens RC, Sali A.

Nat Struct Mol Biol. 2013 Feb;20(2):135-8. doi: 10.1038/nsmb.2508. No abstract available.

11.

Management of healthcare waste: developments in Southeast Asia in the twenty-first century.

Kühling JG, Pieper U.

Waste Manag Res. 2012 Sep;30(9 Suppl):100-4.

PMID:
22993139
12.

Strategic protein target analysis for developing drugs to stop dental caries.

Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD.

Adv Dent Res. 2012 Sep;24(2):86-93. doi: 10.1177/0022034512449837.

13.

Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein.

Puizdar V, Zajc T, Zerovnik E, Renko M, Pieper U, Eswar N, Sali A, Dolenc I, Turk V.

Biol Chem. 2012 Mar;393(3):177-86. doi: 10.1515/hsz-2011-0219.

14.

SALIGN: a web server for alignment of multiple protein sequences and structures.

Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS.

Bioinformatics. 2012 Aug 1;28(15):2072-3. doi: 10.1093/bioinformatics/bts302. Epub 2012 May 21.

15.

Facile backbone structure determination of human membrane proteins by NMR spectroscopy.

Klammt C, Maslennikov I, Bayrhuber M, Eichmann C, Vajpai N, Chiu EJ, Blain KY, Esquivies L, Kwon JH, Balana B, Pieper U, Sali A, Slesinger PA, Kwiatkowski W, Riek R, Choe S.

Nat Methods. 2012 May 20;9(8):834-9. doi: 10.1038/nmeth.2033.

16.

Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.

Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Almo SC, Burley SK.

Proteins. 2012 Aug;80(8):2110-6. doi: 10.1002/prot.24102. Epub 2012 Jun 4.

17.

Paracellular permeability of bronchial epithelium is controlled by CFTR.

Weiser N, Molenda N, Urbanova K, Bähler M, Pieper U, Oberleithner H, Schillers H.

Cell Physiol Biochem. 2011;28(2):289-96. doi: 10.1159/000331742. Epub 2011 Aug 16.

18.

A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae.

Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C.

Mol Cell Proteomics. 2011 Jun;10(6):M110.006478. doi: 10.1074/mcp.M110.006478. Epub 2011 Mar 31.

19.

Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.

Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK.

Proteins. 2011 May;79(5):1672-7. doi: 10.1002/prot.22973. Epub 2011 Mar 1. No abstract available.

20.

ModBase, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. doi: 10.1093/nar/gkq1091. Epub 2010 Nov 19.

21.

Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.

Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A.

Protein Sci. 2010 Nov;19(11):2110-21. doi: 10.1002/pro.491.

22.

Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.

Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK.

Proteins. 2010 Nov 1;78(14):3056-62. doi: 10.1002/prot.22829. No abstract available.

23.

Prediction of protease substrates using sequence and structure features.

Barkan DT, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A.

Bioinformatics. 2010 Jul 15;26(14):1714-22. doi: 10.1093/bioinformatics/btq267. Epub 2010 May 26.

24.

Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145.

Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sauder JM, Burley SK.

Proteins. 2010 Jun;78(8):1992-8. doi: 10.1002/prot.22707. No abstract available.

25.

Comparison of human solute carriers.

Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A.

Protein Sci. 2010 Mar;19(3):412-28. doi: 10.1002/pro.320.

26.

A survey of integral alpha-helical membrane proteins.

Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A.

J Struct Funct Genomics. 2009 Dec;10(4):269-80. doi: 10.1007/s10969-009-9069-8. Epub 2009 Sep 17.

27.

Polynuclear nickel(II) complexes: a magnetostructural study of Ni(II)4, Ni(II)6, and Ni(II)9 species with oxime ligands.

Biswas B, Pieper U, Weyhermüller T, Chaudhuri P.

Inorg Chem. 2009 Jul 20;48(14):6781-93. doi: 10.1021/ic9007608.

PMID:
19552389
28.

A kernel for open source drug discovery in tropical diseases.

Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA.

PLoS Negl Trop Dis. 2009;3(4):e418. doi: 10.1371/journal.pntd.0000418. Epub 2009 Apr 21.

29.

A kernel for the Tropical Disease Initiative.

Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA.

Nat Biotechnol. 2009 Apr;27(4):320-1. doi: 10.1038/nbt0409-320. No abstract available.

30.

Carbanion or amide? First charge density study of parent 2-picolyllithium.

Ott H, Pieper U, Leusser D, Flierler U, Henn J, Stalke D.

Angew Chem Int Ed Engl. 2009;48(16):2978-82. doi: 10.1002/anie.200806221.

PMID:
19288503
31.

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. doi: 10.1007/s10969-008-9056-5. Epub 2009 Feb 14.

32.

Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.

Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD 3rd, Miercke LJ, Giacomini KM, Sali A, Stroud RM.

J Mol Biol. 2009 Jan 23;385(3):820-30. doi: 10.1016/j.jmb.2008.11.021. Epub 2008 Nov 24.

33.

Functional role of the extended loop 2 in the myosin 9b head for binding F-actin.

Struchholz S, Elfrink K, Pieper U, Kalhammer G, Honnert U, Grützner A, Linke WA, Liao W, Bähler M.

J Biol Chem. 2009 Feb 6;284(6):3663-71. doi: 10.1074/jbc.M808338200. Epub 2008 Dec 4.

34.

MODBASE, a database of annotated comparative protein structure models and associated resources.

Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54. doi: 10.1093/nar/gkn791. Epub 2008 Oct 23.

35.

Genomic-scale prioritization of drug targets: the TDR Targets database.

Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL.

Nat Rev Drug Discov. 2008 Nov;7(11):900-7. doi: 10.1038/nrd2684. Epub 2008 Oct 17. Review.

36.

Ligand-derived oxidase activity. Catalytic aerial oxidation of alcohols (including methanol) by Cu(II)-diradical complexes.

Mukherjee C, Pieper U, Bothe E, Bachler V, Bill E, Weyhermüller T, Chaudhuri P.

Inorg Chem. 2008 Oct 6;47(19):8943-56. doi: 10.1021/ic8009767. Epub 2008 Aug 28.

PMID:
18754615
37.

Radical-ligand-derived C-N coupling, Ga(III)-radical vs low-spin Co(III)-radical reactivity.

Chaudhuri P, Bill E, Wagner R, Pieper U, Biswas B, Weyhermüller T.

Inorg Chem. 2008 Jul 7;47(13):5549-51. doi: 10.1021/ic8006348. Epub 2008 May 30.

PMID:
18510307
38.

Comparative protein structure modeling using MODELLER.

Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A.

Curr Protoc Protein Sci. 2007 Nov;Chapter 2:Unit 2.9. doi: 10.1002/0471140864.ps0209s50.

PMID:
18429317
39.

Comparative protein structure modeling using Modeller.

Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A.

Curr Protoc Bioinformatics. 2006 Oct;Chapter 5:Unit-5.6. doi: 10.1002/0471250953.bi0506s15.

40.

Effect of the substituents on the spin coupling between iminosemiquinone pi-radicals mediated by diamagnetic metal ions: l.s. Co(III) vs Ga(III).

Chaudhuri P, Wagner R, Pieper U, Biswas B, Weyhermüller T.

Dalton Trans. 2008 Mar 14;(10):1286-8. doi: 10.1039/b717004a. Epub 2008 Jan 24.

PMID:
18305838
41.

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.

Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S4.

42.

DBAli tools: mining the protein structure space.

Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W393-7. Epub 2007 May 3.

43.

Protein complex compositions predicted by structural similarity.

Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS.

Nucleic Acids Res. 2006 May 31;34(10):2943-52. Print 2006.

44.

MODBASE: a database of annotated comparative protein structure models and associated resources.

Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D291-5.

45.

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A.

Bioinformatics. 2005 Jun 15;21(12):2814-20. Epub 2005 Apr 12.

PMID:
15827081
46.

High-throughput computational and experimental techniques in structural genomics.

Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N.

Genome Res. 2004 Oct;14(10B):2145-54.

47.

MODBASE, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22.

48.

Tools for comparative protein structure modeling and analysis.

Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A.

Nucleic Acids Res. 2003 Jul 1;31(13):3375-80.

49.

ModView, visualization of multiple protein sequences and structures.

Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A.

Bioinformatics. 2003 Jan;19(1):165-6.

PMID:
12499313
50.

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