Fred P Davis

Summary

Affiliation: Howard Hughes Medical Institute
Country: USA

Publications

  1. pmc Transcription factors that convert adult cell identity are differentially polycomb repressed
    Fred P Davis
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia United States of America
    PLoS ONE 8:e63407. 2013
  2. ncbi request reprint Phosphorylation at the interface
    Fred P Davis
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA 20147, USA
    Structure 19:1726-7. 2011
  3. doi request reprint Proteome-wide prediction of overlapping small molecule and protein binding sites using structure
    Fred P Davis
    Howard Hughes Medical Institute, Janelia Farm Research Campus, 19700 Helix Dr, Ashburn, VA 20147, USA
    Mol Biosyst 7:545-57. 2011
  4. pmc The overlap of small molecule and protein binding sites within families of protein structures
    Fred P Davis
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
    PLoS Comput Biol 6:e1000668. 2010
  5. pmc A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas
    Fred P Davis
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
    Bioinformatics 25:1647-54. 2009
  6. pmc Host pathogen protein interactions predicted by comparative modeling
    Fred P Davis
    Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, California 94158, USA
    Protein Sci 16:2585-96. 2007
  7. 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
  8. 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
  9. 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
  10. pmc Structural modeling of protein interactions by analogy: application to PSD-95
    Dmitry Korkin
    Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 2:e153. 2006

Detail Information

Publications15

  1. pmc Transcription factors that convert adult cell identity are differentially polycomb repressed
    Fred P Davis
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia United States of America
    PLoS ONE 8:e63407. 2013
    ..This genomic model of cell identity helps rationalize a growing number of transdifferentiation protocols and may help facilitate the engineering of cell identity for regenerative medicine...
  2. ncbi request reprint Phosphorylation at the interface
    Fred P Davis
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA 20147, USA
    Structure 19:1726-7. 2011
    ..Nishi et al., in this issue of Structure, characterize phosphosites at protein-protein interfaces and estimate the effect of their phosphorylation on interaction affinity, by combining proteomics data with protein structures...
  3. doi request reprint Proteome-wide prediction of overlapping small molecule and protein binding sites using structure
    Fred P Davis
    Howard Hughes Medical Institute, Janelia Farm Research Campus, 19700 Helix Dr, Ashburn, VA 20147, USA
    Mol Biosyst 7:545-57. 2011
    ..Open-source software and the results for several complete proteomes are available at http://pibase.janelia.org/homolobind...
  4. pmc The overlap of small molecule and protein binding sites within families of protein structures
    Fred P Davis
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
    PLoS Comput Biol 6:e1000668. 2010
    ..janelia.org, represent a comprehensive collection of structurally characterized modulators of protein interactions, and suggest that homologous structures are a useful resource for the rational design of interaction modulators...
  5. pmc A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas
    Fred P Davis
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
    Bioinformatics 25:1647-54. 2009
    ..Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest...
  6. pmc Host pathogen protein interactions predicted by comparative modeling
    Fred P Davis
    Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, California 94158, USA
    Protein Sci 16:2585-96. 2007
    ..Our computational method provides a means to mine whole-genome data and is complementary to experimental efforts in elucidating networks of host-pathogen protein interactions...
  7. 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...
  8. 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/)...
  9. 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)...
  10. pmc Structural modeling of protein interactions by analogy: application to PSD-95
    Dmitry Korkin
    Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 2:e153. 2006
    ..More generally, we expect that comparative patch analysis will provide useful spatial restraints for the structural characterization of an increasing number of binary and higher-order protein complexes...
  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. ncbi request reprint PIBASE: a comprehensive database of structurally defined protein interfaces
    Fred P Davis
    Graduate Group in Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, 94143, USA
    Bioinformatics 21:1901-7. 2005
    ..It is composed of binary interfaces extracted from structures in the PDB and the Probable Quaternary Structure server using domain assignments from the Structural Classification of Proteins and CATH fold classification systems...
  13. 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)...
  14. pmc Localization of protein-binding sites within families of proteins
    Dmitry Korkin
    Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143 2552, USA
    Protein Sci 14:2350-60. 2005
    ..Consideration of the binding site localization may also result in spatial restraints for the modeling of protein assembly structures...
  15. pmc Cell type-specific genomics of Drosophila neurons
    Gilbert L Henry
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Nucleic Acids Res 40:9691-704. 2012
    ..Our results suggest that applying INTACT to specific neuronal populations can illuminate the transcriptional regulatory networks that underlie neuronal cell identity...