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Ursula Pieper

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Publications

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Parthasrathy Sampathkumar; J Michael Sauder; David L Stokes; Benjamin L Timney; Paula Upla; Thomas M Weiss; Jeffrey B Bonanno; Stephen K Burley; Javier Fernandez-Martinez; Zhanna Hakhverdyan; Natalia E Ketaren; Seung Joong Kim; Tsutomu Matsui; Jeremy Phillips; Ursula Pieper; William J Rice; Michael P Rout; Andrej Sali; Steven C Almo
Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.
Ursula Pieper; Douglas C Rees; Burkhard Rost; Avner Schlessinger; Raymond C Stevens; David L Stokes; Michael H B Stowell; Robert M Stroud; Michael C Wiener; Geoffrey A Chang; James J Chou; Mark E Dumont; Brian G Fox; Petra Fromme; Wayne A Hendrickson; Edda Kloppmann; Michael G Malkowski; Andrej Sali
Coordinating the impact of structural genomics on the human α-helical transmembrane proteome.
Hannes Braberg; Ursula Pieper; Andrej Sali; Elina Tjioe; Benjamin M Webb; Mallur S Madhusudhan
SALIGN: a web server for alignment of multiple protein sequences and structures.

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All Publications

2013: Parthasrathy Sampathkumar; J Michael Sauder; David L Stokes; Benjamin L Timney; Paula Upla; Thomas M Weiss; Jeffrey B Bonanno; Stephen K Burley; Javier Fernandez-Martinez; Zhanna Hakhverdyan; Natalia E Ketaren; Seung Joong Kim; Tsutomu Matsui; Jeremy Phillips; Ursula Pieper; William J Rice; Michael P Rout; Andrej Sali; Steven C Almo
Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.
Structure (London, England : 1993) 2013;21(4):560-71.
2013: Ursula Pieper; Douglas C Rees; Burkhard Rost; Avner Schlessinger; Raymond C Stevens; David L Stokes; Michael H B Stowell; Robert M Stroud; Michael C Wiener; Geoffrey A Chang; James J Chou; Mark E Dumont; Brian G Fox; Petra Fromme; Wayne A Hendrickson; Edda Kloppmann; Michael G Malkowski; Andrej Sali
Coordinating the impact of structural genomics on the human α-helical transmembrane proteome.
Nature structural & molecular biology 2013;20(2):135-8.
2012: Hannes Braberg; Ursula Pieper; Andrej Sali; Elina Tjioe; Benjamin M Webb; Mallur S Madhusudhan
SALIGN: a web server for alignment of multiple protein sequences and structures.
Bioinformatics (Oxford, England) 2012;28(15):2072-3.
2012: Parthasrathy Sampathkumar; J Michael Sauder; Devon A Thompson; Hiro Tsuruta; Stephen R Wasserman; Steven C Almo; Shane Atwell; Kevin T Bain; J Spencer Emtage; Javier Fernandez-Martinez; Josef D Franke; Tarun Gheyi; Jeremiah Gilmore; Seung Joong Kim; Danalyn Manglicmot; Tsutomu Matsui; Jeremy Phillips; Ursula Pieper; Michael P Rout; Andrej Sali; Stephen K Burley
Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.
Proteins 2012;80(8):2110-6.
2012: Vida Puizdar; Miha Renko; Andrej Sali; Iztok Dolenc; Narayanan Eswar; Ursula Pieper; Tajana Zajc; Eva Zerovnik; Vito Turk
Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein.
Biological chemistry 2012;393(3):177-86.
2011: Ursula Pieper; Benjamin M Webb; David T Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C Meng; Eric F Pettersen; Conrad C Huang; Ruchira S Datta; Parthasrathy Sampathkumar; Mallur S Madhusudhan; Kimmen Sjölander; Thomas E Ferrin; Stephen K Burley; Andrej Sali
ModBase, a database of annotated comparative protein structure models, and associated resources.
Nucleic acids research 2011;39(Database issue):D465-74.
2010: Libusha Kelly; Hisayo Fukushima; Rachel Karchin; Jason M Gow; Leslie W Chinn; Ursula Pieper; Mark Segal; Deanna L Kroetz; Andrej Sali
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.
Protein science : a publication of the Protein Society 2010;19(11):2110-21.
2010: David T Barkan; Daniel R Hostetter; Sami Mahrus; Ursula Pieper; James A Wells; Charles S Craik; Andrej Sali
Prediction of protease substrates using sequence and structure features.
Bioinformatics (Oxford, England) 2010;26(14):1714-22.
2010: Avner Schlessinger; Pär Matsson; James E Shima; Ursula Pieper; Sook Wah Yee; Libusha Kelly; Leonard Apeltsin; Robert M Stroud; Thomas E Ferrin; Kathleen M Giacomini; Andrej Sali
Comparison of human solute carriers.
Protein science : a publication of the Protein Society 2010;19(3):412-28.
2009: Libusha Kelly; Ursula Pieper; Narayanan Eswar; Franklin A Hays; Min Li; Zygy Roe-Zurz; Deanna L Kroetz; Kathleen M Giacomini; Robert M Stroud; Andrej Sali
A survey of integral alpha-helical membrane proteins.
Journal of structural and functional genomics 2009;10(4):269-80.
2009: Ursula Pieper; Ranyee Chiang; Jennifer J Seffernick; Shoshana D Brown; Margaret E Glasner; Libusha Kelly; Narayanan Eswar; J Michael Sauder; Jeffrey B Bonanno; Subramanyam Swaminathan; Stephen K Burley; Xiaojing Zheng; Mark R Chance; Steven C Almo; John Alan Gerlt; Frank M Raushel; Matthew P Jacobson; Patricia C Babbitt; Andrej Sali
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
Journal of structural and functional genomics 2009;10(2):107-25.
2009: Min Li; Franklin A Hays; Zygy Roe-Zurz; Linda Vuong; Libusha Kelly; Chi-Min Ho; Renée M Robbins; Ursula Pieper; Joseph D O'Connell; Larry J W Miercke; Kathleen M Giacomini; Andrej Sali; Robert M Stroud
Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.
Journal of molecular biology 2009;385(3):820-30.
2007: Narayanan Eswar; Ben Webb; maricus MR; Mallur S Madhusudhan; David Eramian; Min-Yi Shen; Ursula Pieper; Andrej Sali
Comparative protein structure modeling using MODELLER.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2007;Chapter 2():Unit 2.9.
2007: maricus MR; Ursula Pieper; Mallur S Madhusudhan; Andrea Rossi; Narayanan Eswar; Fred P Davis; Fátima Al-Shahrour; Joaquín Dopazo; Andrej Sali
DBAli tools: mining the protein structure space.
Nucleic acids research 2007;35(Web Server issue):W393-7.
2007: maricus MR; Andrea Rossi; Fátima Al-Shahrour; Fred P Davis; Ursula Pieper; Joaquín Dopazo; Andrej Sali
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
BMC bioinformatics 2007;8 Suppl 4():S4.
2006: Narayanan Eswar; Ben Webb; maricus MR; Mallur S Madhusudhan; David Eramian; Min-Yi Shen; Ursula Pieper; Andrej Sali
Comparative protein structure modeling using Modeller.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2006;Chapter 5():Unit 5.6.
2006: Fred P Davis; Hannes Braberg; Min-Yi Shen; Ursula Pieper; Andrej Sali; Mallur S Madhusudhan
Protein complex compositions predicted by structural similarity.
Nucleic acids research 2006;34(10):2943-52.
2006: Ursula Pieper; Narayanan Eswar; Fred P Davis; Hannes Braberg; Mallur S Madhusudhan; Andrea Rossi; maricus MR; Rachel Karchin; Ben M Webb; David Eramian; Min-Yi Shen; Libusha Kelly; Francisco Melo; Andrej Sali
MODBASE: a database of annotated comparative protein structure models and associated resources.
Nucleic acids research 2006;34(Database issue):D291-5.
2005: Rachel Karchin; Mark Diekhans; Libusha Kelly; Daryl J Thomas; Ursula Pieper; Narayanan Eswar; David Haussler; Andrej Sali
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Bioinformatics (Oxford, England) 2005;21(12):2814-20.
2004: Mark R Chance; András Fiser; Andrej Sali; Ursula Pieper; Narayanan Eswar; Guiping Xu; Jorge Fajardo; Thirumuruhan Radhakannan; Nebojsa Marinkovic
High-throughput computational and experimental techniques in structural genomics.
Genome research 2004;14(10B):2145-54.
2004: Ursula Pieper; Narayanan Eswar; Hannes Braberg; Mallur S Madhusudhan; Fred P Davis; Ashley C Stuart; Nebojsa Mirkovic; Andrea Rossi; maricus MR; András Fiser; Ben Webb; Daniel Greenblatt; Conrad C Huang; Thomas E Ferrin; Andrej Sali
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic acids research 2004;32(Database issue):D217-22.
2003: Narayanan Eswar; Bino John; Nebojsa Mirkovic; András Fiser; Valentin A Ilyin; Ursula Pieper; Ashley C Stuart; maricus MR; Mallur S Madhusudhan; Bozidar Yerkovich; Andrej Sali
Tools for comparative protein structure modeling and analysis.
Nucleic acids research 2003;31(13):3375-80.
2003: Valentin A Ilyin; Ursula Pieper; Ashley C Stuart; maricus MR; Linda McMahan; Andrej Sali
ModView, visualization of multiple protein sequences and structures.
Bioinformatics (Oxford, England) 2003;19(1):165-6.
2002: Mark R Chance; Anne R Bresnick; Stephen K Burley; Jian-Sheng Jiang; Christopher D Lima; Andrej Sali; Steven C Almo; Jeffrey B Bonanno; John A Buglino; Simon J Boulton; Hua Chen; Narayanan Eswar; Guoshun He; Raymond Huang; Valentin A Ilyin; Linda McMahan; Ursula Pieper; Soumya Ray; Marc Vidal; Li Kai Wang
Structural genomics: a pipeline for providing structures for the biologist.
Protein science : a publication of the Protein Society 2002;11(4):723-38.
2002: Ursula Pieper; Narayanan Eswar; Ashley C Stuart; Valentin A Ilyin; Andrej Sali
MODBASE, a database of annotated comparative protein structure models.
Nucleic acids research 2002;30(1):255-9.
2001: Jeffrey B Bonanno; C Edo; Narayanan Eswar; Ursula Pieper; Michael J Romanowski; Valentin A Ilyin; Sue Ellen Gerchman; Helen Kycia; F William Studier; Andrej Sali; Stephen K Burley
Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(23):12896-901.
2001: Shuba Gopal; M Schroeder; Ursula Pieper; Alexander Sczyrba; G Aytekin-Kurban; Stefan Bekiranov; Jorge Fajardo; Narayanan Eswar; R Sanchez; Andrej Sali; Terry Gaasterland
Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.
Nature genetics 2001;27(3):337-40.
2000: R Sánchez; Ursula Pieper; Francisco Melo; Narayanan Eswar; MA Martí-Renom; Mallur S Madhusudhan; N Mirković; Andrej Sali
Protein structure modeling for structural genomics.
Nature structural biology 2000;7 Suppl():986-90.
2000: R Sánchez; Ursula Pieper; N Mirković; P I de Bakker; E Wittenstein; Andrej Sali
MODBASE, a database of annotated comparative protein structure models.
Nucleic acids research 2000;28(1):250-3.