Ursula Pieper

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
    Marc A Marti-Renom
    Structural Genomics Unit, Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    BMC Bioinformatics 8:S4. 2007
  2. pmc Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA 94158, USA
    J Struct Funct Genomics 10:107-25. 2009
  3. pmc MODBASE: a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 34:D291-5. 2006
  4. pmc DBAli tools: mining the protein structure space
    Marc A Marti-Renom
    Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158 2330, USA
    Nucleic Acids Res 35:W393-7. 2007
  5. pmc MODBASE, a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 37:D347-54. 2009
  6. pmc MODBASE, a database of annotated comparative protein structure models, and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 32:D217-22. 2004
  7. doi request reprint Comparative protein structure modeling using Modeller
    Narayanan Eswar
    University of California at San Francisco, San Francisco, California, USA
    Curr Protoc Bioinformatics . 2006
  8. pmc A survey of integral alpha-helical membrane proteins
    Libusha Kelly
    Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, CA, USA
    J Struct Funct Genomics 10:269-80. 2009
  9. pmc SALIGN: a web server for alignment of multiple protein sequences and structures
    Hannes Braberg
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:2072-3. 2012
  10. doi request reprint Comparative protein structure modeling using MODELLER
    Narayanan Eswar
    University of California at San Francisco, San Francisco, California, USA
    Curr Protoc Protein Sci . 2007

Detail Information

Publications19

  1. pmc The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
    Marc A Marti-Renom
    Structural Genomics Unit, Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    BMC Bioinformatics 8:S4. 2007
    ..Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database...
  2. pmc Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA 94158, USA
    J Struct Funct Genomics 10:107-25. 2009
    ....
  3. pmc MODBASE: a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 34:D291-5. 2006
    ..org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP)...
  4. pmc DBAli tools: mining the protein structure space
    Marc A Marti-Renom
    Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158 2330, USA
    Nucleic Acids Res 35:W393-7. 2007
    ..Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions...
  5. pmc MODBASE, a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 37:D347-54. 2009
    ..MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/)...
  6. pmc MODBASE, a database of annotated comparative protein structure models, and associated resources
    Ursula Pieper
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 32:D217-22. 2004
    ..org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb)...
  7. doi request reprint Comparative protein structure modeling using Modeller
    Narayanan Eswar
    University of California at San Francisco, San Francisco, California, USA
    Curr Protoc Bioinformatics . 2006
    ..Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described...
  8. pmc A survey of integral alpha-helical membrane proteins
    Libusha Kelly
    Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, CA, USA
    J Struct Funct Genomics 10:269-80. 2009
    ....
  9. pmc SALIGN: a web server for alignment of multiple protein sequences and structures
    Hannes Braberg
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:2072-3. 2012
    ..All features of the server have been previously optimized for accuracy, especially in the contexts of comparative modeling and identification of interacting protein partners...
  10. doi request reprint Comparative protein structure modeling using MODELLER
    Narayanan Eswar
    University of California at San Francisco, San Francisco, California, USA
    Curr Protoc Protein Sci . 2007
    ..Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described...
  11. pmc Protein complex compositions predicted by structural similarity
    Fred P Davis
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California San Francisco, 1700 4th Street, Byers Hall, San Francisco, CA 94143 2552, USA
    Nucleic Acids Res 34:2943-52. 2006
    ..cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE (http://salilab.org/modbase)...
  12. pmc ModBase, a database of annotated comparative protein structure models, and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158, USA
    Nucleic Acids Res 39:D465-74. 2011
    ..org/modeval), the PCSS server for predicting which peptides bind to a given protein (http://salilab.org/pcss) and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles (http://salilab.org/foxs)...
  13. ncbi request reprint LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
    Rachel Karchin
    Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Bioinformatics 21:2814-20. 2005
    ..SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity...
  14. pmc Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains
    Libusha Kelly
    Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, California, USA
    Protein Sci 19:2110-21. 2010
    ..Our analysis provides a structural and evolutionary framework for rationalizing and predicting the functional effects of nsSNPs in this clinically important membrane transporter superfamily...
  15. pmc Prediction of protease substrates using sequence and structure features
    David T Barkan
    Graduate Group in Bioinformatics, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
    Bioinformatics 26:1714-22. 2010
    ..Our approach can act as a convenient hypothesis generator, guiding future experiments by high-confidence identification of peptide-protein partners...
  16. doi request reprint ModBase, a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Graduate Group in Biophysics, University of California at San Francisco, CA 94158, USA, Structural Bioinformatics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France, Universite Paris Diderot Paris 7, ├ęcole doctorale iViv, Paris Rive Gauche, 5 rue Thomas Mann, 75013 Paris, France, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Life Sciences Division, Department of Molecular Biology, Stanford
    Nucleic Acids Res 42:D336-46. 2014
    ....
  17. pmc Comparison of human solute carriers
    Avner Schlessinger
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, California
    Protein Sci 19:412-28. 2010
    ..The classification scheme will inform future attempts directed at modeling the structures of the solute carriers, a prerequisite for describing the substrate specificities of the individual families...
  18. pmc Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening
    Min Li
    Membrane Protein Expression Center, University of California at San Francisco, San Francisco, CA 94158 2517, USA
    J Mol Biol 385:820-30. 2009
    ..This discovery-oriented pipeline provides an efficient way to select proteins from particular membrane protein classes, families, or organisms that may be more suited to structure analysis than others...
  19. pmc Tools for comparative protein structure modeling and analysis
    Narayanan Eswar
    Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 31:3375-80. 2003
    ....