Valerie Daggett, PhD

Professor, Bioengineering

Adjunct Professor, Biochemistry

Adjunct Professor, Biomedical Informatics and Medical Education

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

Daggett Research Group


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


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]