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Paper of the Month

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

Beck, D.A.C, Jonsson, A.L., Schaeffer, R.D., Scott, K.A., Day, R., Toofanny, R.D., Alonso, D.O.V., and V. Daggett
Protein Engineering Design & Selection (2008) In Press

The goal of Dynameomics is to perform atomistic molecular dynamics (MD) simulations of representative proteins from all known folds in explicit water in their native state and along their thermal unfolding pathways. Here we present 188-fold representatives and their native state simulations and analyses. more...


Goals: Realistic simulation of protein dynamics, unfolding/folding, conformational transitions linked to disease, and the design of biomaterials

Latest News

  • The Daggett Lab was awarded 10 million processor hours for 2008 on the Department of Energy's supercomputers! The National Energy Research Scientific Computing Center (NERSC), located in Berkeley, CA, is one of the largest computing facilities in the world for basic scientific research.
  • The Benjamin Hall Interdisciplinary Research Building, one of only 11 Gold-level green buildings in the US, is the new home of the Daggett Lab.
  • The Daggett Group's work on prion protein was referenced in the September issue of Wellcome Trust's Big Pictures Series on Epidemics. [PDF]
  • The work on prion protein was again cited in the August Issue of Chemical and Engineering News.
  • The Dynameomics project and potential startup company was featured in the Biomedical Computation Review article "Biocomputation Startups: Where Does Value Lie?" by Katharine Miller. [PDF]
  • The Department of Energy awarded the Daggett group 2 million processor hours in 2005 through an Innovative and Novel Computational Impact on Theory and Experiment Award (INCITE), one of 3 awards in the country, for the Molecular Dynameomics project. [DOE press release]
    • Update: The NERSC Annual Report feature, "Proteins in Motion," details the Daggett group's Dynameomics Project.
    • Update: The Department of Energy has awarded the Daggett group an additional 1.9 million processor hours at NERSC for 2006!
  • Now you can download Powerpoint slides of our prion conversion trajectory. If you want to know how your experimental data compare with our model or you want specific figures or analyses email us.
  • The Dynameomics project was the subject of a recent article in The Scientist, "Unraveling Protein Folding" by Melissa Lee Phillips. [PDF]
  • The Daggett Group's work on amyloid disease was the subject of recent editorials in Science by Orla Smith [PDF] and in Nature by Christopher Surridge. [PDF]

Daggett Group
Department of Bioengineering
University of Washington
Foege Building N310B, Box 355061
1705 NE Pacific Street
Seattle, WA 98195-5061

616 NE Northlake Place, Suite 300H
Seattle, WA 98105

daglab@u.washington.edu