David A. C. Beck The author of in lucem Molecular Mechanics (ilmm). Senior Research Scientist eScience Institute University of Washington Ph.D. Biomolecular Structure & Design / Medicinal Chemistry University of Washington

Publications | top

• Beck D.A.C., Alonso D.O.V., Inoyama D., and Daggett V. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proceedings of the National Academy of Sciences USA 105: 12259-12264, 2008. [DOI]
• McCully M.E., Beck D.A.C., and Daggett V. Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain. Biochemistry 47: 7079-7089, 2008. [DOI]
• Smolin N., Li B., Beck D.A.C., and Daggett V. Side-chain dynamics are critical for water permeation through aquaporin-1. Biophysical Journal 95:1089-1098, 2008. [DOI]
• 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. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. Protein Engineering Design & Selection, 21, 353-368, 2008. [DOI]

• Beck, D.A.C. and V. Daggett. A One-Dimensional Reaction Coordinate for Identification of Transition States from Explicit Solvent P_fold-Like Calculations. Biophysical Journal, 93, 8832-3391, 2007. [HTML] [PDF]
• Beck, D.A.C., Bennion, B.J., Alonso, D.O.V and V. Daggett. Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics. Methods in Enzymology, 428, 373-396, 2007. [DOI]
• Beck, D.A.C., White, G.W.N., and V. Daggett, Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Journal of Structural Biology, 157, 514-523, 2007. [DOI]
• Beck, D.A.C., Armen, R.S. and V. Daggett, Cutoff size need not strongly influence molecular dynamics results on solvated polypeptides. Biochemistry, 44, 609-616, 2005. [DOI] (#12 most cited paper for Biochemistry in 2005)
• Beck, D.A.C. and V. Daggett, Methods for Molecular Dynamics Simulations of Protein Folding/Unfolding in Solution, Methods, 34, 112-120, 2004. [DOI]
• Day, R., Beck, D.A.C., Armen, R. and V. Daggett, A Consensus View of Fold Space: Combining SCOP, CATH, and the Dali Domain Dictionary, Protein Science, 12, 2150-2160, 2003. [DOI]
• Beck, D.A.C., Alonso, D.O.V. and V. Daggett. A microscopic view of peptide and protein solvation. Biophysical Chemistry 100, 221-237, 2003. [DOI]

Research | top

• Design, implementation and development of in lucem Molecular Mechanics (ilmm), a scalable parallel molecular mechanics engine for:
  • drug design and docking
  • protein design
  • molecular dynamics (MD) simulation of proteins in:
    • explicit solvent (water),
    • explicit co-solvents such as water, urea, gndHCl, TMAO, etc. or mixtures of these
    • membranes or anchored to membranes (via GPI)
    • replica exchange (REMD)
    • probability of folding (Pfold) calculations
  • analysis of MD simulations, including:
    • structure comparison (RMSD, CONGENEAL)
    • dihedral reporting and Phi/Psi statistics
    • solvent accessible surface area (SASA)
    • indentification of intra and intermolecular contacts
    • NMR NOE, order parameters (S2) and residual dipolar coupling (RDC)
    • diffusion, radial distribution function, solvent density function
    • and much, much, more...
  • other features:
    • minimization
    • simulated annealing
    • replica-exchange molecular dynamics (REMD)
    • distance geometry
    • embedded versions for use in Perl and Python
    • direct interfaces to UCSF Chimera and Pymol
  
  
• MD studies of fold space representative proteins: Dynameomics
  • All atom, explicit solvent native and thermal unfolding simulations for 251 target proteins whose folds represent about 80% of the known protein domains
  • For more information, see our website: http://www.dynameomics.org
  
  
• Bridging the gap between experiment and MD with long timescale MD studies of fast folding protein systems, including:
  • Protein A, E-domain
  • Engrailed Homeodomain
  
  
• Co-solvent development and testing

Molecular Dynamics movies | top

• 1huu_movie.mpg (dimer & monomer side by side, interesting conformational change)
• 1erd_498.mpg (1erd folding/unfolding)
• 1ev4_298.mpg (1ev4 monomer native state)
• 1qcv_498.mpg (1qcv folding/unfolding)
• 4pga_498.mpg (4pga folding/unfolding)
• 3chy_native.mpg (3chy native state)
• 3chy_fold.mpg (3chy folding/unfolding)
• aquaporin.mpg (bovine aquaporin in membrane, water channel in action, 259 MB! many browsers find this too big to play)

David A. C. Beck
eScience Institute
University of Washington, Box 359562
UW Tower O2-248
4333 Brooklyn Ave NE
Seattle, WA 98195
Phone: 206 221 0709
Fax: 206 543 5884

© David A. C. Beck 2009