Valerie Daggett, PhD

Professor, Bioengineering

Adjunct Professor, Biochemistry

Adjunct Professor, BIME

B.A. Reed College, PhD UCSF, Postdoctoral Fellow, Standord University

daggett@uw.edu

Daggett Research Group


Interests:

Data management and representation, database, mining techniques, visual analytics, structural bioinformatics, protein folding and design, single-nucleotide polymorphisms, Dynameomics.

Background:

25 yrs molecular modeling proteins/peptides. Dr. Daggett is on the editorial boards: Biochemistry, Structure, and Biomedical Computation Review (BCR). Senior Editor: Protein Engineering, Design, and Selection. Founding member of the Biomolecular Structure and Design Program. Editor of a 2003 volume on Protein Simulations for Advances in Protein Chemistry. Member of NIH Macromolecular Structure and Function B Study Section, July 2005 – 2008. Biophysical Society Fellow, 2011. Funded Research: a) Molecular dynamics simulations of protein unfolding (NIH)| b)  Characterization of prion protein conformational changes (NIH)| c)  Design and characterization of alpha-sheet compounds (NSF, CART, NIH)| d) Data exploration and visualization (Microsoft)| and e) Molecular Dynameomics (DOE).  Member of the Board of Reviewing Editors of eLife.

Representative publications:

  • Van der Kamp M.W., Schaeffer R.D., Jonsson A.L., Scouras A.D., Simms A.M., Toofanny R.D., Benson N.C., Anderson P.C., Merkley E.D., Rysavy S., Bromley D., Beck D.A.C., and Daggett V. Dynameomics: A Comprehensive Database of Protein Dynamics. Structure 18:423-435, 2010.[DOI]
  • Schaeffer R.D, Jonsson A.L., Simms A.M., and Daggett V. Generation of a Consensus Protein Domain Dictionary. Bioinformatics 27:46-54, 2011. [DOI]
  • Toofanny, R.D., Simms, A.M., Beck, D.A.C. and V. Daggett, Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection. BMC Bioinformatics, 12:334, 2011. [DOI]
  • Benson, N.C. and V. Daggett, Wavelet Analysis of Protein Motion. Int. J. Wavelets, Multiresol. Info. Processing, 10:1250040, 2012. [DOI]
  • Simms, A.M. and V. Daggett, Protein simulation data in the relational model. J. of Supercomp. In press: 1-24, 2011. [DOI]
  • Benson N.C. and Daggett V.  A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations.  Journal of Physical Chemistry B, 116, 8722-8731, 2012. [DOI]
  • Benson N.C. and Daggett V.  A Chemical Group Graph Representation for Efficient High-Throughput Analysis of Atomistic Protein Simulations.  Journal of Bioinformatics and Computational Biology 10:1250008-1250024, 2012. [DOI]