Interests:

Structural bioinformatics, databases, mining techniques, visual analytics, protein folding and design, single-nucleotide polymorphisms, amyloid diseases, protein design, dynameomics combined with experimental biophysical studies, diagnostic and therapeutic design for amyloid diseases.

Background:

B.A. Chemistry, Reed College, Ph.D. Pharmaceutical Chemistry, UC San Francisco, Jane Coffin Childs Postdoctoral Fellow in Structural Biology, Stanford University, 30 yrs molecular modeling and biophysical studies of proteins/peptides. Performed first molecular dynamics simulations of protein folding/unfolding, single-nucleotide polymorphisms, and conformational changes during amyloidogenesis. Dr. Daggett is on the editorial boards of Biochemistry, Structure, and Current Opinion in Structural Biology. Formerly Senior Editor: Protein Engineering, Design, and Selection. Biophysical Society Fellow, elected 2011, Fellow of the American Institute of Medical and Biological Engineering, elected 2017.

Research:

Our molecular dynamics simulations led to the discovery of a new protein structure formed early during amyloidogenesis linked to toxicity. Computational simulations and associated informatics studies progressed to experimental studies to test the computational predictions and to diagnostic and therapeutic development efforts based on the computational and informatics findings. Current research involves protein simulations, structural informatics, protein design, and associated experimental studies.

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 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]
• Bromley, D., Daggett, V. Tumorigenic p53 Mutants Undergo Common Structural Disruptions Including Conversion to a-Sheet Structure, Sci., 29: 1983-1999, 2020.
• Prosswimmer, T., Daggett, V. The role of a-sheet structure in amyloidogenesis: characterization and implications. Royal Society, Open Biology, 2: 91-110, 2022.
• Shea, D., Colasurdo, E., Smith, Al., Paschall, C., Jayadev, S., Keene, C.D., Galasko, D., Do, A., Li, G., Peskind, E., Daggett, V., SOBA: Development and Testing of a Soluble Oligomer Binding Assay for Detection of Amyloidogenic Toxic Oligomers, Natl. Acad. Sci. USA, 119(50), e2213157119, 2022.
  • This paper received considerable attention, including mention from 220 news outlets, from Bloomberg to health-related magazines. In addition, it was featured in January in “NIH Research Matters”.
  • Received GeekWire Health Innovation of the Year Award for SOBA, 2023
  • Featured on the Wikipedia Timeline of Biotechnology, 2022 for SOBA AD diagnostic, citing PNAS 2022
  • Featured on the Wikipedia 2022 in Science, for SOBA AD diagnostic, citing PNAS 2022
• Bleem, A. Prosswimmer, T., Chen, R., Hady, T., Li, J., Bryers, J.D., Daggett, V. Designed α-sheet peptides disrupt uropathogenic  coli biofilms rendering bacteria susceptible to antibiotics and immune cells, NPJ Scientific Reports, 13, 9297, 2023.