个人简介

B.S. in Chemistry, Michigan State University A.M. in Physics, Harvard University Ph.D. in Chemical Physics, Harvard University Honors President's Award, International Society of Quantum Biology and Pharmacology, 2014. American Chemical Society Award for Computers in Chemical and Pharmaceutical Research, 2015

研究领域

Biophysical Chemistry/Physical Chemistry

Theoretical chemistry of biomolecules. Particular areas of interest include molecular dynamics simulations of proteins and nucleic acids; electronic structure calculations of transition-metal complexes that model active sites in metalloenzymes; development and application of methods for NMR structure determination; ligand-protein and ligand-nucleic acid docking and computational drug design.

近期论文

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G.M. Giambaşu, T. Luchko, D. Herschlag, D.M. York and D.A. Case. Ion counting from explicit solvent simulations and 3D-RISM. Biophys. J., 104, 883-894 (2014). H. Nguyen, S.A. Pabitt, S. Meisburger, L. Pollack and D.A. Case. Accurate small and wide angle X-ray scattering profiles from atomic models of proteins and nucleic acids. J. Chem. Phys. 114, 22D508 (2014). D.S. Cerutti, W.C. Swope, J.E. Rice and D.A. Case. ff14ipq: A self-consistent force field for condensed-phase simulations of proteins. J. Chem. Theory Comput. 10, 4515-4534 (2014). M. Pasi, J.H. Maddocks, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham III, B. Jayaram, F. Lankas, C. Laughton, J. Mitchel, R. Osman, M. Orozco, D. Petkeviciute, N. Spackova, J. Sponer, K. Zakrzewska and R. Lavery. microABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucl. Acids Res. 42, 12272-12283 (2014). C. Liu, P.A. Janowski and D.A. Case. All-atom crystal simulations of DNA and RNA duplexes. Biochim. Biophys. Acta (in press) T.E. Cheatham, III and D.A. Case. Twenty-five years of nucleic acid simulations. Biopolymers, 99, 969-977 (2013). X. Wu, S. Subramaniam, D.A. Case, K. Wu and B.R. Brooks. Map constrained self-guided Langevin dynamics. J. Struct. Biol. 183, 429-440 (2013). P.A. Janowski, D.S. Cerutti, J. Holton and D.A. Case. Peptide crystal simulations reveal hidden dynamics. J. Am. Chem. Soc. 135, 7938-7948 (2013). D.A. Case. Chemical shifts in biomolecules. Curr. Opin. Struct. Biol. 23, 172-176 (2013). D.S. Cerutti, J.E. Rice, W. Swope, and D.A. Case. Derivation of fixed partial charges for amino acid analogs accommodating a specific water model and implicit polarization. J. Phys. Chem. B 117, 2328-2338 (2013). D. Mitra, S. George, J. Peters, S. Keable, V. Pelmenschikov, D.A. Case, and S.P. Cramer. Dynamics of the [4Fe-4S] cluster in Azotobacter vinelandii nitrogenase Fe protein in three core oxidation states via nuclear resonance vibrational spectroscopy (NRVS). J. Am. Chem. Soc. 135, 2530-2543 (2013). I.S. Joung, T. Luchko and David A. Case. Simple electrolyte solutions: Comparison of RISM and molecular dynamics results for alkali halide solutions. J. Chem. Phys. 138, 044103 (2013). R. Salomon-Ferrer, D.A. Case and R.C. Walker. An overview of the Amber biomolecular simulation package. WIREs: Comput. Mol. Sci., 3, 198-210 (2013). J. Latzer, T. Steinbrecher and D.A. Case. Revised AMBER parameters for bioorganic phosphates. J. Chem. Theory Comput. 8, 4405-4412 (2012). T. Luchko, I.S. Joung and D.A. Case. Integral equation theory of biomolecules and electrolytes. In Innovations in Biomolecular Modeling and Simulation, Volume 1. T. Schlick, ed. (London, Royal Society of Chemistry, 2012), pp. 51-86. T. Steinbrecher, D.A. Case and A. Labahn. Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. Bioorg. Med. Chem. 20, 3446-3453 (2012). S.R. Brozell, S. Mukherjee, T.E. Balius, D.R. Roe, D.A. Case and R.C. Rizzo. Evaluation of DOCK 6 as a pose generation and database enrichment tool. J. Comput. Aided Mol. Des. 26, 749-773 (2012). J.D. Kim, A. Godriguez-Ganillo, D.A. Case, V. Nanda and P.G. Falkowski. Energetic selection of topology in ferredoxins. PLoS Comput. Biol. 8, e1002463 (2012). T. Luchko and D.A. Case. Implicit solvent models and electrostatics in molecular recognition. In: Protein-Ligand Interactions, H. Gohlke, ed. (Weinheim, Germany: Wiley-VCH, 2012), pp. 171-189. J. Xia and D.A. Case. Sucrose in aqueous solution revisited. 1. Molecular dynamics simulations and direct and indirect dipolar coupling analysis. Biopolymers 97, 276-288 (2012). J. Xia and D.A. Case. Sucrose in aqueous solution revisited. 2. Adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation. Biopolymers, 97, 289-302 (2012). R. Chaudhuri, S. Tang, G. Zhao, H. Lu, D.A. Case and M.E. Johnson. Comparison of SARS and NL63 papain-Like protease binding sites and binding site dynamics: Inhibitor design implications. J. Mol. Biol. 414, 272-288 (2011). J. Xia, C.J. Margulis and D.A. Case. Searching and optimizing structure ensembles for complex flexible sugars. J. Am. Chem. Soc. 133, 15252-15255 (2011). T. Gaillard and D.A. Case. Evaluation of DNA force fields in implicit solvation. J. Chem. Theory Comput. 7, 3181-3198 (2011). S. Tang and D.A. Case. Calculation of chemical shift anisotropy in proteins. J. Biomol. NMR 51, 303-312 (2011). I. Bertini, D.A. Case, L. Ferella, A. Giachetti and A. Rosato. A grid-enabled web portal for NMR structure refinement with AMBER. Bioinformatics, 27, 2384-2390 (2011). T. Steinbrecher, I.S. Joung and D.A. Case. Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations. J. Comput. Chem. 32, 3253-3263 (2011). D. Mitra, V. Pelmenschikov, Y. Guo, D.A. Case, H. Wang, W. Dong, M. Tan, T. Ichiye, F. Jenney, Jr., M.W.W. Adams, M. Kaupp and S.P. Cramer. Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus Ferredoxin via Nuclear Resonance Vibrational Spectroscopy (NRVS) and Resonance Raman Spectroscopy – Quantitative Simulation by Density Functional Theory. Biochemistry, 50, 5220-5235 (2011). V. Pelmenschikov, Y. Guo, H. Wang, S.P. Cramer and D.A. Case. Fe-H/D stretching and bending modes in nuclear resonant vibrational, Raman and infrared spectroscopies: Comparisons of density functional theory and experiment. Faraday Disc., 148, 409-420 (2011). D.A. Case. In silico: An alternate approach to chemistry and biology. In Letters to a Young Chemist, A. Ghosh, ed. (New York: John Wiley & Sons, 2011), pp. 19-31. R. Lavery, K. Zakrzewska, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham, III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, N. Spackova and J. Sponer. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res. 38: 299-313 (2010). D.S. Cerutti and D.A. Case. Multi-level Ewald: A scalable variant of traditional Ewald mesh methods. J. Chem. Theory Comput. 6, 443-459 (2010). T. Luchko, S. Gusarov, D.R. Roe, C. Simmerling, D.A. Case, J. Tuszynski and A. Kovalenko. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. J. Chem. Theory Comput. 6, 607-624 (2010). B.S. Tolbert, Y. Miyazaki, S. Barton, B. Kinde, P. Starck, R. Singh, A. Bax, D.A. Case and M.F. Summers. Major groove width variations in RNA structures determined by NMR and impact of 13 C residual chemical shift anisotropy and 1 H-13 C residual dipolar coupling on refinement. J. Biomol. NMR 47, 205-219 (2010). K.F. Wong, F. Paesani, J.L. Sonnenberg, T. Yamamoto, J. Vanicek, W. Zhang, H.B. Schlegel, D.A. Case, T.E. Cheatham, III, W.H. Miller and G.A. Voth. Proton Transfer Studied Using a Reactive Potential Energy Surface Combined with Quantum Path Integrals. J. Chem. Theory Comput. 6, 2566-2580 (2010). D.S. Cerutti, P.L. Freddolino, R.E. Duke and David A. Case. Simulations of a protein crystal with a high resolution X-ray structure: Evaluation of force fields and water models. J. Phys. Chem. B 114, 12811-12824 (2010).