Related Publications

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General Description of Dynameomics

• Van der Kamp MW, Schaeffer RD, Jonsson AL, Scouras AD, Simms AM, Toofanny RD, Benson NC, Anderson PC, Merkley ED, Rysavy S, Bromley D, Beck DAC, and Daggett V. Dynameomics: A comprehensive database of protein dynamics. Structure, 18: 423-435, 2010. [DOI]
• Beck, DAC, Jonsson AL, Schaeffer RD, Scott KA, Day R, Toofanny RD, Alonso DOV, Daggett V. 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]

Consensus Domain Dictionary

• Schaeffer RD, Jonsson A, Simms AM, and Daggett V. Generation of a consensus domain dictionary and fold representative selection. Submitted for Publication, 2010
• Day R, Beck DA, Armen RS, and Daggett V. A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary. Protein Science, 12: 2150-2160, 2003. [DOI]

Database

• Simms AM, Toofanny RD, Kehl C, Benson NC, and Daggett V. Dynameomics: Design of a computational lab workflow and scientific data repository for protein simulations. Protein Engineering Design & Selection, 21: 369-377, 2008. [DOI]
• Kehl C, Simms AM, Toofanny RD, and Daggett V. Dynameomics: A multi-dimensional analysis-optimized database for dynamic protein data. Protein Engineering Design & Selection, 21: 379-386, 2008. [DOI]

Papers Making Use of Dynameomics Data

• Toofanny RD, Jonsson A, and Daggett V. A comprehensive one-dimensional reaction coordinate for protein unfolding/folding. Biophysical Journal, 98:2671-2681, 2010. [DOI]
• Law P and Daggett V. The relationship between water bridges and the polyproline II conformation: A large-scale analysis of molecular dynamics simulations and crystal structures. Protein Engineering Design & Selection, 23: 27-33, 2010. [DOI]
• Jonsson AL, Scott KA, and Daggett V. Dynameomics: A consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. Biophysical Journal, 97: 2958-2966, 2009. [DOI]
• Key J, Scheuermann TH, Anderson PC, Daggett V, and Gardner KH. Principles of ligand binding within a completely buried cavity in HIF2α PAS-B. Journal of American Chemical Society, 131: 17647-17654, 2009. [DOI]
• Calderon CP and Arora K. Extracting kinetic and stationary distribution information from short MD trajectories via a collection of surrogate diffusion models. Journal of Chemical Theory Computation, 5: 47-58, 2009. [DOI]
• Beck DAC, Alonso DOV, 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]
• Benson N and Daggett V. Dynameomics: Large-scale assessment of native protein flexibility. Protein Science, 17: 2038-2050, 2008. [DOI]
• Scott KA, Alonso DOV, Sato S, Fersht AR, and Daggett V. Conformational entropy of alanine versus glycine in protein denatured states. Proceedings of the National Academy of Sciences USA, 104: 2661-2666, 2007. [DOI]

Papers Making Use of SNP Data

• Rutherford K and Daggett V. The V119I polymorphism in protein L-isoaspartate O-methyltransferase alters the substrate-binding interface. Protein Engineering Design & Selection, 22: 713-721, 2009. [DOI] [Color Figures]
• Rutherford K and Daggett V. A hotspot of inactivation: The A22S and V108M polymorphisms individually destabilize the active site structure of catechol O-methyltransferase. Biochemistry, 48: 6450-6460, 2009. [ DOI ]
• Schmidlin T, Kennedy B, and Daggett V. Structural changes to monomeric CuZn superoxide dismutase caused by the familial Amyotrophic Lateral Sclerosis mutation A4V. Biophysical Journal, 97: 1709-1718, 2009. [DOI]
• Anderson PC and Daggett V. The R46Q, R131Q and R154H polymorphs of human DNA glycosylase/β-lyase hOgg1 severely distort the active site and DNA recognition site but do not cause unfolding. Journal of the American Chemical Society, 131: 9506-15, 2009. [DOI]
• Anderson PC and Daggett V. Molecular basis for the structural instability of human DJ-1 induced by the L166P mutation associated with Parkinson's disease. Biochemistry, 47: 9380-9393, 2008. [DOI]
• Rutherford K and Daggett V. Four human thiopurine S-methyltransferase alleles severely affect protein structure and dynamics. Journal of the American Chemical Society, 379: 803-814, 2008. [DOI]
• Rutherford K, Parson WW, and Daggett V. The histamine N-methyltransferase T105I polymorphism affects active site structure and dynamics. Biochemistry, 47: 893-901, 2008. [DOI]
• Rutherford K, Bennion BJ, Parson WW, and Daggett V. The 108M polymorph of human catechol O-methyltransferase is prone to deformation at physiological temperatures. Biochemistry, 45: 2178-2188, 2006. [DOI]

Papers Making Use of Consensus Domain Dictionary

• Rueda M, Ferrer-Costa C, Meyer T, Pérez A, Camps J, Hospital A, Gelpí JL, and Orozco M. A consensus view of protein dynamics. Proceedings of the National Academy Science USA,104: 796-801, 2007. [DOI]
• Meyer T, de la Cruz X, and Orozco M. An atomistic view to the gas phase proteome. Structure 17: 88-95, 2009. [DOI]

Press

• Research Highlight on Van der Kamp et al. Nature Methods, 2010. [DOI]
• Hules J. Proteins in motion. National Energy Research Scientific Computing Center Annual Report: Research News, 2005. [Article]
• Phillips ML. Unraveling protein folding. The Scientist, 2005. [PDF]