Dr. David Snyder



Post-Doctoral Study 2006-2008 Florida State University, National High Magnetic Field Lab

Ph.D. 2006, Rutgers University, NJ

B.S. 1999, Mathematics and Biology, University of Calfornia, Irvine

Research Interests

Proteins are molecular machines that bind specific ligands, fold into particular shapes and flex in specific ways in order to function. Nuclear Magnetic Resonance (NMR) is a powerful technique for obtaining information about a protein’s conformation, dynamics and binding partners. However, NMR experiments are often limited in sensitivity and resolution. My research focuses on how to use computational techniques to maximally leverage data obtained in NMR experiments as well as on how to interpret the imprecision of NMR-derived protein structures in terms of protein dynamics. Additionally, my research group is developing bio-informatics based approaches to predict protein flexibility in order to better understand how changes in protein dynamics mediate the evolution of protein function.

Selected Publications

Analysis of ligand–protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP). D.A. Snyder, M. Chantova and S. ChaudhryJ. Magn. Reson. 2015, 255, 44-50.

The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction. D.A. Snyder, Y. J.Huang, R. Tejero and G. T. Montelione. Proteins: Struct. Funct. Bioinformatics, 2014, 82 (S2), 219-230.

Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. D.A Snyder, et al.  Proteins: Struct. Funct. Bioinformatics. 2012, 80, 1901-1906.

A covariance NMR toolbox for MATLAB and OCTAVE. T. ShortL. Alzapiedi, R. Brüschweiler and D.A. Snyder. J. Magn. Reson.  2011, 209, 75-78.

Z-matrix formalism for quantitative noise assessment of covariance nuclear magnetic resonance spectra David A. Snyder, et alJ. Chem. Phys. 2008, 129, 104511.

Resolution-Enhanced 4D 15N/ 13C-NOESY Protein NMR Spectroscopy by Application of the Covariance Transform David A. Snyder, et alJ. Am. Chem. Soc. 2007, 129, 14126-14127.

Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins. David A. Snyder, et alJ. Biomol NMR. 2007, 39, 165-175.

Lack of correlation between NMR spectral quality and success in crystallization demonstrates that NMR and X-ray crystallography are complementary methods for small protein structure determination D.A. Snyder, et al.J. Am. Chem. Soc. 2005, 127, 16505-16511. (Cited in Nature: News and Views).

Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles David A. Snyder and Gaetano T. Montelione.Proteins: Struct. Funct. Bioinformatics. 2005, 59, 673-686. (Cover Article)