BA College of Wooster MAA Wesleyan University PHD University Cincinnati

Molecular Dynamics and Monte Carlo Computer Simulation; Structure, Dynamics and Solvation of Nucleic Acids and Proteins, Affinity and Specificity of Ligand Binding, Protein-Nucleic Acid Recognition.

Dixit, S.B, and Beveridge, D.L, (2006) “Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction,” Bioinformatics Applications Notes, Vol. 22 (8) 1007-1009.

Dixit, S.B., Ponomarev, S.Y., and Beveridge, D.L., (2006) “Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA,” J Chem Inf Model, 46, 1084-1093. Hatchell, E.C., S.M. Colley, et al. (2006). “SLIRP, a small SRA binding protein, is a nuclear receptor compressor.” Mol Cell 22(5): 657-68

Kormos, B.L., Baranger, A.M. and Beveridge, D.L. (2006) Do collective atomic fluctuations account for cooperative effects? Molecular dynamic studies of U1A-RNA complex. J AM Chem Soc, 128, 8992-8993.

Zhao, Y., Kormos, B.L., Beveridge, D.L. and Baranger, A.M. (2006) Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface.Biopolymers, 81, 256-269.

Kormos, B.L., Baranger, A.M. and Beveridge, D.L. (2007) A Study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations. J. Struc. Biol., 157, 500-513.

Kormos, B.L., Benitex, Y., Baranger, A.M. and Beveridge, D.L. (2007) Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model. J Mol Biol, 371, 1405-1419.

Yan, Z., Sikri, S., Beveridge, D.L. and Baranger, A.M. (2007) Identification of an aminoacridine derivative that binds to RNA tetraloops. J Med Chem, 50, 4096-4104.

hong, W., Dixit, S. B., Mallis, R. J., Arthanari, H., Lugovskoy, A. A., Beveridge, D. L., Wagner, G. & Reinherz, E. L. (2007). CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implications. J Mol Biol 372, 535-48.

Anunciado, D., Agumeh, M., Kormos, B. L., Beveridge, D. L., Knee, J. L. & Baranger, A. M. (2008). Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements. J Phys Chem B 112, 6122-30.

Knee, K. M., Dixit, S. B., Aitken, C. E., Ponomarev, S., Beveridge, D. L. & Mukerji, I. (2008). Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA. Biophys J 95, 257-72.

Saunus, J. M., J.D. French, et al. (2008). “Posttranscriptional regulation of the breast cancer susceptibility gene BRCA1 by the RNA binding protein HuR.” Cancer Res 68(22):9469-78

Singhal, P., Jayaram, B., Dixit, S. B. & Beveridge, D. L. (2008). Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 94, 4173-83.

Sen, S., Andreatta, D., Ponomarev, S. Y., Beveridge, D. L. & Berg, M. A. (2009). Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. J Am Chem Soc 131, 1724-35.

Lavery, R., Zakrzewska, K., Beveridge, D., Bishop, T. C., Case, D. A., Cheatham, T., 3rd, Dixit, S., Jayaram, B., Lankas, F., Laughton, C., Maddocks, J. H., Michon, A., Osman, R., Orozco, M., Perez, A., Singh, T., Spackova, N. & Sponer, J. (2010). A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformat. Nucleic Acids Res. 38, 299-313.

Kormos, B. L. Pieniazek, S., Beveridge, D.L. (2010) U1A Protein -Stem Loop 2 RNA Recognition: Structural Differences in F56 Mutants from MD Simulations, Biopolymers, .

Pieniazek, S. Hingorani, M., Beveridge, (2011) D.L. Dynamical Allosterism in a Mismatch Repair Protein, MutS, Biophysical Journal, 101, 1730-9.

Wheatley, E.G., Pieniazek, S.N., Mukerji, I., Beveridge, D.L, (2012) Molecular dynamics of a DNA Holliday junction: the inverted repeat sequence d(CCGGTACCGG)(4), Biophys J. 102, 552-60.

Beveridge, D.L., Cheatham, T.E., 3rd, Mezei, M., (2012) The ABCs of molecular dynamics simulations on B-DNA, circa 2012, J. Biosci. 37, 379-97.

Dixit, S.B., Mezei, M., Beveridge, D.L. (2012) Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations, J Biosci., 37, 399-421.

Khandelwal, G., Lee, R.A., Jayaram, B., Beveridge, D.L. (2014) A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes, Biophys. J., 106, 2465-73.