Ursula Pieper
Associate Researcher, Sali Lab
Publications
  1. U. Pieper, R. Chiang, J.J. Seffernick, S.D. Brown, M.E. Glasner, N. Eswar, M. Sauder, S.K. Burley, S. Almo, J.A. Gerlt, F. Raushel, B.K. Shoichet, M.P. Jacobson, P.P. Babbitt, A. Sali. Target Selection and Annotation for the Structural Genomics of Enolases and Amidohydrolases. submitted.
  2. L. Kelly, U. Pieper, F. Hays, N. Eswar, D. Kroetz, K. Giacomini, R. Stroud, A. Sali. A taxonomic profile of the membrane protein universe . submitted.
  3. F. Aguero, B. Al-Lazikani, BerrimanM. , F.S. Buckner, CampbellB. , s. Carmona, FengChen, G. CrowtherJ, C. Hertz-Fowler, A.L. Hopkins, G. McAllister, S. Nwaka, OveringtonJ. , A. Pain, G.V. Paolini, U. Pieper, S.A. Ralph, A. Riechers, D.S. Roos, A. Sali, D. Shanmugam, T. Suzuki, W.C. VanVoorhis, C.L. Verlinde. Genomic-scale Prioritization of Drug Targets: TDRtargets.org. submitted.
  4. N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M-Y. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling Using MODELLER. Ed: Coligan JE, Dunn BM, Speicher DW, Wingfield PT. Current Protocols in Protein Science Unit 2.9 1-31.
  5. U. Pieper, M.S Madhusudhan, A. Rossi, N. Eswar, F.P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali. DBAli tools: mining the protein structure space. Nucleic Acids Research 35, W393-W397, 2007.
  6. A. Rossi, F. Al-Shahrour, F.P. Davis, U. Pieper, J. Dopazo, A. Sali. The AnnoLite and AnnoLyze Programs for Comparative Annotation of Protein Structures. BMC Bioinformatics 8 Suppl 4, 2007.
  7. Braberg, M.Y. Shen, U. Pieper, A. Sali, M.S. Madhusudhan. Protein complex compositions predicted by structural similarity. Nucleic Acids Research 34, 2943-2952, 2006.
  8. Marti-Renom, B. Webb, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling using MODELLER. Ed: Baxevanis AD, Petsko GA, Stein LD, Stormo GD. Current Protocols in Bioinformatics John Wiley & Sons, Inc., Hoboken, NJ, Supplement 15, 5.6.1-5.6.30, 2006.
  9. F.P. Davis, H. Braberg, M.S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B.M. Webb, D. Eramian, M.Y. Shen, L. Kelly, F. Melo, A. Sali. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research 34, D291-D295, 2006.
  10. L. Kelly, D.J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali. LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 21, 2814-2820, 2005.
  11. A. Marti-Renom, N. Eswar, B. John, U. Pieper, R. Karchin, Min-yi Shen, A. Sali. Comparative Protein Structure Modeling. In: The Proteomics Protocols Handbook. Ed: J.M. Walker. Humana Press Inc., Totowa, NJ, 831-860, 2005.
  12. Fiser, A. Sali, U. Pieper, N. Eswar, G. Xu, E. Fajardo, T. Radhakannan, N. Marinkovic. High-Throughput Computational and Experimental Techniques in Structural Genomics. Genome Research 14, 2145-2154, 2004.
  13. H. Braberg, M.S. Madhusudhan, F. Davis, A.C. Stuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, C. Huang, T. Ferrin, A. Sali. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Research 32, D217-D222, 2004.
  14. A. Fiser, M.S. Madhusudhan, B. John, A. Stuart, N. Eswar, P. Pieper, M-Y. Shen, A. Sali. Modeling protein structure from its sequence. Current Protocols in Bioinformatics John Wiley & Sons, Inc., Hoboken, NJ, V. 5 November Issue, Pages 5.1.1-5.1.32, 2003.
  15. N. Mirkovic, A. Fiser, V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, M.S. Madhusudhan, B. Yerkovich, A. Sali. Tools for comparative protein structure modeling and analysis. Nucleic Acids Research 31, 3375-3380, 2003.
  16. R. Chance, S.K. Burley, J. Jiang, S.C. Almo, A. Bresnick, T. Dodatko, R. Huang, G. He, H. Chen, M. Sullivan, J. Toomey, R.A. Thirumuruhan, W.A. Franklin, A. Sali, U. Pieper, N. Eswar, V. Ilyin, L. McMahan. Structural Genomics at the National Synchrotron Light Source. NSLS Activity Report 2001 2, 28-32, 2002.
  17. R. Bresnick, S.K. Burley, J.S. Jiang, C.D. Lima, A. Sali, S.C. Almo, J.B. Bonanno, J.A. Buglino, S. Boulton, H. Chen, N. Eswar, G. He, R. Huang, V. Ilyin, L. McMahan, U. Pieper, S. Ray, M. Vidal, L.K. Wang. Structural Genomics: A pipeline for providing structures for the biologist. Protein Science 11, 723-738, 2002.
  18. A.C. Stuart, V.A. Ilyin, A. Sali. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research 30, 255-259, 2002.
  19. Pieper, A.C. Stuart, M.A. Marti-Renom, L. McMahan, A. Sali. ModView, visualization of multiple protein sequences and structures. Bioinformatics 19, 165-166, 2003.
  20. Edo, N. Eswar, U. Pieper, M.J. Romanowski, V. Ilyin, S.E. Gerchman, H. Kycia, F.W. Studier, A. Sali, S.K. Burley. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. PNAS 98, 12896-12901, 2001.
  21. U. Pieper, A. Sczyrba, G. Aytekin-Kurban, S. Bekiranov, E.J. Fajardo, N. Eswar, R. Sanchez, A. Sali, T. Gaasterland. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat. Genet. 27, 337-340, 2001.
  22. F. Melo, N. Eswar, M.A. Marti-Renom, M.S. Madhusudhan, N. Mirkovic, A. Sali. Protein structure modeling for structural genomics. Nat. Struct. Biol. 7, 986-990, 2000.
  23. N. Mirkovic, P.I.W. deBakker, E. Wittenstein, A. Sali. MODBASE, a database of annotated comparative protein structure models. Nucl. Acids Res. 28, 250-253, 2000.
  24. Ursula Pieper, Geeta Kapadia, Moshe Mevarech, Osnat Herzberg, Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea archeaon Haloferax volcanii Structure 6 (1998), 75-88.
  25. Soojay Banerjee, Ursula Pieper, Geeta Kapadia, J.K.Pennel, Osnat Herzberg, The role of the omega-loop in the activity, substrate specificity and structure of class A b-lactamase Biochemistry 37 (1998), 3286-3296.
  26. Ursula Pieper, Koto Hayakawa, Zhong Li, Osnat Herzberg, Circularly permuted b-lactamase from Staphylococcus aureus PC1 Biochemistry 36 (1997), 8767-8774.
  27. Ursula Pieper, Geeta Kapadia, Peng-Peng Zhu, Alan Peterkofsky, Osnat Herzberg, Structural evidence for the evolutionary divergence of mycoplasma from Gram-positive bacteria: the histidine-containing phosphocarrier protein, Structure, 3 (1995), 781-790.
  28. Heike Voelker, Stefanie Freitag, Ursula Pieper, Herbert W. Roesky, Synthesis of the new Silanediyldiphosphinite tBu2Si(OPPH2)2 and its reactions with the norbornadiene complexes C7H8M(CO)4 (M=Cr, Mo, W). Crystal structures of cis-M(CO)4tBu2Si(OPPh2)2 (M=Cr, Mo) Z. Anorg. Allg. Chem. 621 (1995), 694-698.
  29. Andrea Frenzel, Uwe Klingebiel, Wolfgang Luttke, Ursula Pieper, Synthese von 1,2-Bis(silyl)indolen unter anionischer 1,2-Silatropie J. Organomet. Chem. 476 (1994), 73-76.
  30. Hans-Otto Frohlich, Ralf Wyrwa, Helmar Gorls, Ursula Pieper, Eine ungewohnliche Koordinationsgeometrie des Platin(II) in dem homoleptischen Metallacyclopentankomplex [Li(PMDETA)]2Pt-CH2CH2CH2CH2)2 J. Organomet. Chem. 471 (1994) 23-27.
  31. Anne Grunhagen, Ursula Pieper, Thomas Kottke, Herbert W. Roesky, Synthesen und Strukturen funktionell substituierter Ferrocene Z. anorg. allg. Chemie 620 (1994), 716-722.
  32. Daniele Hoffmann, Walter Bauer, Frank Hampel, Nicolaas J.R. van Eikema Hommes, Paul von Rague Schleyer, Peter Otto, Ursula Pieper, Dietmar Stalke, Dominic S. Wright and Ron Snaith, h3 and h6 bridging cations in the N, N, N, N,N-pentamethyldiethylenetriamine-solvated complexes of benzylpotassium and benzylrubidium: an X-ray, NMR, and MO study J. Am. Chem. Soc. 116 (1994), 528-536.
  33. Heike Voelker, Ursula Pieper, Herbert W. Roesky, George M. Sheldrick, Darstellung und Struktur von 2,3-Bis[2,4,6-tris(trifluoromethyl)phenyl]- 1,2,3-selenadiphosphiran Z. Naturforsch. 49b (1994), 255-257.
    34. 15. Melanie Rieckhoff, Ursula Pieper, Dietmar Stalke, Ansa-metallocenes of calcium and strontium one-pot synthesis of organometallic complexes of the heavier alkaline-earth metals Angew. Chem. Int. Ed. 32 (1993), 1079-1081.
  34. Ursula Pieper and Dietmar Stalke, Synthesis and X-ray structures of diphenylpyridylmethyllithium, -sodium and -potassium in comparison with the triphenylmethyl derivatives Organimetallics 12 (1993), 1201-1206.
  35. Daniele Hoffmann, Walter Bauer, Paul von Rague Schleyer, Ursula Pieper and Dietmar Stalke, Kation-induced structural alterations in the organo alkali metal derivatives of triphenylmethane, combined X-ray and NMR study of the K-Cs salts Organometallics 12 (1993), 1193-1200.
  36. Michael Wedler, Friedrich Knosel, Ursula Pieper, Dietmar Stalke, Frank T. Edelmann und Hanns-Dieter Amberger, Sterische Cyclopentadienyl Aquivalente in der Chemie der f-Elemente: Monomere, homoleptische Lanthanid(III)-tris[N,N-bis(trimethylsilylbenzamidinate] Chem. Ber. 125 (1992), 2171-2181.
  37. Steffen Schutte, Ursula Pieper, Uwe Klingebiel, Dietmar Stalke, A stable aquo-complex of lithiated di-tert.butyl-fluorsilanol after the first step of hydrolysis - synthesis and crystal structure J. Organomet. Chem. 446 (1993), 45-49.
  38. Christoph Lambert, Paul von Rague Schleyer, Ursula Pieper, Dietmar Stalke, Wasser als Ligand in lithiierten organischen Verbindungen [LiCH(CN)2xH2OxTMEDA] Angew. Chem. 104 (1992), 78.
  39. Anja Recknagel, Mathias Noltemeyer, Dietmar Stalke, Ursula Pieper, Hans Georg Schmidt, Frank T. Edelmann, Monomere Organosamarium(III)chalkogenolate durch reduktive Spaltung von E-E-Bindungen (E=S, Se, Te) J. Organomet. Chem. 411 91991), 346-356.
  40. Michael Wedler, John W. Gilje, Ursula Pieper, Dietmar Stalke, Mathias Noltemeyer, Frank T. Edelmann, Losliche Lanthanidalkoxide mit niedrigen Koordinationszahlen am Metallatom Chem. Ber. 124 (1991), 1163-1165.
  41. Thomas Kottke, Uwe Klingebiel, Mathias Noltemeyer, Ursula Pieper, Simone Walter, Dietmar Stalke, Vom Lithium-Derivat des Amino-di-tert.-Butylfluorsilans zu Cyclodi-, tri- und tetrasilazenen Chem. Ber. 124 (1991), 1941-1945.
  42. Uwe Klingebiel, Matthias Meyer, Ursula Pieper, Dietmar Stalke, Lithium-bis(di- tert-butyl fluorsilyl)phosphid - ein cyclisches Zwitterion J. Organomet. Chem. 408 (1991), 19-25.
  43. Michael Wedler, Mathias Noltemeyer, Ursula Pieper, Hans-Georg Schmidt, Dietmar Stalke, Frank T. Edelmann, Ytterbium(II)benamidinate, eine neue Klasse hochreaktiver Lanthanoid(II)komplexe Angew. Chem. 102 (1990), 941.
  44. Dietmar Stalke, Ursula Pieper, Susanne Vollbrecht, Uwe Klingebiel, Lithium-Iminofluorsilan und Natrium-Floursilylamid - ein Vergleich Z. Naturforsch. B45 (1990), 1513-1515.
  45. Ursula Pieper, Dietmar Stalke, Susanne Vollbrecht, Uwe Klingebiel, Natrium- und Kaliumfluorsilylamide - Synthese und Kristallstruktur Chem. Ber. 123 (1990), 1039-1041.
  46. Ursula Pieper, Simone Walter, Uwe Klingebiel, Dietmar Stalke,Lithium-bis (di-tert-butyl fluorsilyl)amid als Kontaktionenpaar mit linearer Si-N--Si-Einheit und als Ionenpaar ohne Li-Anion-Kontakt Angew. Chem. 102 (1990), 218-219.
  47. Hans H. Karsch, Brigitte Deubelly, Josef Hofmann, Ursula Pieper, Gerhard Muller, h1 - coordination versus h2- coordination in transition-metal phosphinomethanide complexes: synthesis and X-ray structure of Cp2Zr(Cl)[C(PMe2)SiMe3)2) J. Am. Chem. Soc. 110 (1988), 3654-3657.