David A. C. Beck
University of Washington |
Department of Chemical Engineering |
Table of Contents:
Media (movies & figures) |
Research | top
- Metagenomics & systems biology of microbial cultures and communities
- Pathway reconstruction and analysis of bacterial communities from *omics datasets with relevance to
- biogeochemical cycling,
- the microbiome and health of built environments and,
- human health
- Development of techniques for analysis, comparison, and unification of transcriptomics and proteomics datasets
- Biophysical chemistry software, methods and applications (see more below)
- Author of in lucem Molecular Mechanics (ilmm, Beck, D.A.C., Alonso, D.O.V., & Daggett, V)
- Development of an XML schema for molecular mechanics parameter library: MMPL
- Methods and software development for in silico drug and protein design in high-performance computing (HPC) environments
- Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
- All atom, explicit solvent native and thermal unfolding simulations for hundreds of target proteins whose folds represent about 80% of the known protein domains
- For more information, see our website: http://www.dynameomics.org
- Workflow design and engineering for data-intensive analytics in biology and chemistry
- Data mining, management and sharing strategies for large biological datasets
Features of in lucem Molecular Mechanics:
- in lucem Molecular Mechanics (ilmm) is 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:
- simulated annealing
- replica-exchange molecular dynamics (REMD)
- distance geometry
- embedded versions for use in Perl and Python
- direct interfaces to UCSF Chimera and Pymol
Professional Service | top
- Computer in Biology and Medicine (Elsevier Journal), Editorial Board Member
- National Energy Research Scientific Computer Center (NERSC) User's Group Executive Committee (NUGEX) representative for Office of Biology and Environmental Research (Retired)
Publications | top
Kalyuzhnaya, M.G., Yang, S., Rozova, O.N., Smalley, N.E., Clubb, J., Lamb A., Nagana Gowda G.A., Raftery, D., Fu, Y., Bringel F., Vuilleumier, S., Beck, D.A.C., Trotsenko, Y.A., Khmelenina, V.N., and Lidstrom, M.E. (2013) Highly Efficient Methane Biocatalysis Revealed in a Methanotrophic Bacterium. Nature Comm. In press.
Beck D.A.C., Kalyuzhnaya M.G., Malfatti S., Tringe S., Glavina del Rio T., Ivanova N., Lidstrom M. E., Chistoserdova L. (2013) A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 1:e23.
Khmelenina V. N., Beck D.A.C., Munk C., et al. (2013) Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium. Genome Announc. Jul-Aug; 1(4): e00053-13.
Vorobev A., Beck D.A.C., Kalyuzhnaya M.G., Lidstrom M. E., Chistoserdova L. (2013) Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation. PeerJ 1:e115.
- Yang S., Matsen J.B., Konopka M., Green-Saxena A., Clubb J., Sadilek M., Orphan V.J., Beck, D.A.C., and M.G. Kalyuzhnaya. Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study. Front. Microbiol., 03 April 2013.
- Matsen J.B., Yang S., Stein L.Y., Beck, D.A.C., and M.G. Kalyuzhnaya. Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: transcriptomic study. Front. Microbiol., 03 April 2013.
- McCully M.E., Beck D.A.C., Daggett V. Multimolecule test-tube simulations of protein unfolding and aggregation. Proceedings of the National Academy of Sciences USA, 109:17851-17856 2012. [DOI]
- McCully M.E., Beck D.A.C., Daggett V. Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain. Protein Engineering & Selection, Online: 2012. [DOI]
- Hirano T.*, Beck D.A.C.*, Wright C.J., Demuth D.R., Hackett M., Lamont R.J. Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis. Mol Oral Microbiol., Sep 20, Epub, 2012. *Contributed equally.
- Hirano T.*, Beck D.A.C.*, Demuth D.R., Hackett M., Lamont R.J. Deep Sequencing of Porphyromonas gingivalis and Comparative Transcriptome Analysis of a LuxS Mutant. Front Cell Infect Microbiol., 2:79, 2012. *Contributed equally.
- Toofanny, R.D., Simms, A., Beck, D.A.C., and V. Daggett. Implementation of3D spatial hashing in a large-scale molecular dynamics simulation database for rapid atomic contact detection. BMC Bioinformatics, 12:334, 2011. [DOI]
- Beck, D.A.C., Hendrickson, E.L., Vorobev, A., Wang, T., Lim, S., Kalyuzhnaya, M.G., Lidstrom, M.E., Hackett, M., Chistoserdova, L. An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis. J Bacteriol. 2011, Jul 15.
- Kittichotirat W, Good NM, Hall R, Bringel F, Lajus A, Médigue C, Smalley NE, Beck D, Bumgarner R, Vuilleumier S, Kalyuzhnaya MG. Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales. J. Bacteriol. 193(17):4541-2, 2011.
- Lapidus A., Clum A., Labutti K., Kaluzhnaya M.G., Lim S., Beck D.A.C., Glavina Del Rio T., Nolan M., Mavromatis K., Huntemann M., Lucas S., Lidstrom M.E., Ivanova N., Chistoserdova L. Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae. J Bacteriol. 193(15):3757-64, 2011.
- Kalyuzhnaya, M.G., Beck, D.A.C., and L. Chistoserdova. Functional metagenomics of methylotrophs. Methods in Enzymology, 495:81-98, 2011.
- Ojala, D.S., Beck, D.A.C., and M.G. Kalyuzhnaya. Genetic tools for moderately halo(alkali)philic bacteria of the genus Methylomicrobium. Methods in Enzymology, 495:99- 118, 2011.
- Barga, R., Howe, B., Beck, D.A.C., Bowers, S., Dobyns, W., Haynes, W., Higdon, R., Howard, C., Roth, C., Stewart, E., Welch, D., and Kolker, E. Bioinformatics and Data-Intensive Scientific Discovery. OMICS, 15(4), 2011.
- McCully M.E., Beck D.A.C., Fersht A.R., and Daggett V. Refolding the Engrailed Homeodomain: Structural Basis for the Accumulation of a Folding Intermediate. Biophysical Journal 99:1628-1636, 2010. [DOI]
- 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] [Cover Image]
- Research Highlight on this paper in Nature Methods. [DOI]
- Hendrickson E.L., Beck D.A.C., Wang T., Lidstrom M. E., Hackett. M., and L. Chistoserdova. The expressed genome of Methylobacillus flagellatus defined through proteogenomics and new insights into methylotrophy. Journal of Bacteriology, 192: 4859-4867, 2010.[DOI]
- Kalyuzhnaya, M.G., Beck, D.A.C., Suciu, D., Pozhitkov, A., Lidstrom M.E., and L. Chistoserdova. Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed via transcriptomics. ISME Journal, 4: 388-398, 2009.
- 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 Pfold-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]
Media (figures and movies) | top
Molecular Dynamics movies
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Links | top
Alphabetical list of links to collaborators and related sites:
David A. C. Beck
Benjamin Hall IRB, Rm 400
UW Box 355014
Seattle, WA 98195
Phone: 206 221 0709
© David A. C. Beck 2009-2013