Publications

  1. Schriber, J. B.; Sirianni, D. A.; Flanagin, G.; Parish, C. A.; Miller, B. R. I. Building a Successful Computational Chemistry Laboratory. In Physical Chemistry Research at Undergraduate Institutions: Innovative and Impactful Approaches, Volume 1; ACS Symposium Series; American Chemical Society, 2022; Vol. 1428, pp 69–83. https://doi.org/10.1021/bk-2022-1428.ch005.
  2. Prins, R.; Windsor, P.; Miller III, B. R.; Maiden, S. Alleles of Unc-33/CRMP Exhibit Defects during Caenorhabditis Elegans Epidermal Morphogenesis. Dev. Dyn. 2022, 251 (10), 1741–1753. https://doi.org/10.1002/dvdy.497.
  3. Yim, W.; Takemura, K.; Zhou, J.; Zhou, J.; Jin, Z.; Borum, R. M.; Xu, M.; Cheng, Y.; He, T.; Penny, W.; Miller, B. R. I.; Jokerst, J. V. Enhanced Photoacoustic Detection of Heparin in Whole Blood via Melanin Nanocapsules Carrying Molecular Agents. ACS Nano 2022, 16 (1), 683–693. https://doi.org/10.1021/acsnano.1c08178.
  4. Souza, S. A.; Held, A.; Lu, W. J.; Drouhard, B.; Avila, B.; Leyva-Montes, R.; Hu, M.; Miller, B. R.; Ng, H. L. Mechanisms of Allosteric and Mixed Mode Aromatase Inhibitors. RSC Chem. Biol. 2021, 2 (3), 892–905. https://doi.org/10.1039/D1CB00046B.
  5. Windsor, P. K.; Plassmeyer, S. P.; Mattock, D. S.; Bradfield, J. C.; Choi, E. Y.; Miller, B. R.; Han, B. H. Biflavonoid-Induced Disruption of Hydrogen Bonds Leads to Amyloid-β Disaggregation. Int. J. Mol. Sci. 2021, 22 (6), 2888. https://doi.org/10.3390/ijms22062888.
  6. Ojaghlou, N.; Airas, J.; McRae, L. M.; Taylor, C. A.; Miller, B. R. I.; Parish, C. A. Understanding the Structure and Apo Dynamics of the Functionally Active JIP1 Fragment. J. Chem. Inf. Model. 2021, 61 (1), 324–334. https://doi.org/10.1021/acs.jcim.0c01008.
  7. Case, H. B.; Mattock, D. S.; Miller, B. R. I.; Dickenson, N. E. Novel Noncompetitive Type Three Secretion System ATPase Inhibitors Shut Down Shigella Effector Secretion. Biochemistry 2020, 59 (28), 2667–2678. https://doi.org/10.1021/acs.biochem.0c00431.
  8. Modeste, E.; Mawby, L.; Miller, B. I.; Wu, E.; Parish, C. A. A Molecular Dynamics Investigation of the Thermostability of Cold-Sensitive I707L KlenTaq1 DNA Polymerase and Its Wild-Type Counterpart. J. Chem. Inf. Model. 2019, 59 (5), 2423–2431. https://doi.org/10.1021/acs.jcim.9b00022.
  9. Wang, J.; Jeevarathinam, A. S.; Humphries, K.; Jhunjhunwala, A.; Chen, F.; Hariri, A.; Miller, B. R. I.; Jokerst, J. V. A Mechanistic Investigation of Methylene Blue and Heparin Interactions and Their Photoacoustic Enhancement. Bioconjug. Chem. 2018, 29 (11), 3768–3775. https://doi.org/10.1021/acs.bioconjchem.8b00639.
  10. Yeager, A.; Humphries, K.; Farmer, E.; Cline, G.; Miller, B. R. Investigation of Nascent Base Pair and Polymerase Behavior in the Presence of Mismatches in DNA Polymerase I Using Molecular Dynamics. J. Chem. Inf. Model. 2018, 58 (2), 338–349. https://doi.org/10.1021/acs.jcim.7b00516.
  11. Yeager, A. V.; Swails, J. M.; Miller, B. R. I. Improved Accuracy for Constant PH-REMD Simulations through Modification of Carboxylate Effective Radii. J. Chem. Theory Comput. 2017, 13 (10), 4624–4635. https://doi.org/10.1021/acs.jctc.7b00638.
  12. Wang, W.; Taylor, C.; Hu, H.; Humphries, K. L.; Jaini, A.; Kitimet, M.; Scott, T.; Stewart, Z.; Ulep, K. J.; Houck, S.; Luxon, A.; Zhang, B.; Miller, B.; Parish, C. A.; Pomerantz, A. E.; Mullins, O. C.; Zare, R. N. Nanoaggregates of Diverse Asphaltenes by Mass Spectrometry and Molecular Dynamics. Energy Fuels 2017, 31 (9), 9140–9151. https://doi.org/10.1021/acs.energyfuels.7b01420.
  13. Beane, A.; Miller, B. R.; Parish, C. A. Internal Abstraction of Dynemicin A: An MD Approach. J. Mol. Graph. Model. 2017, 74, 251–264. https://doi.org/10.1016/j.jmgm.2017.03.012.
  14. Taylor, C. A.; Miller, B. R.; Parish, C. A. Design and Computational Support for the Binding Stability of a New CCR5/CXCR4 Dual Tropic Inhibitor: Computational Design of a CCR5/CXCR4 Drug. J. Mol. Graph. Model. 2017, 75, 71–79. https://doi.org/10.1016/j.jmgm.2017.02.012.
  15. Taylor, C. A.; Miller, B. R.; Shah, S. S.; Parish, C. A. A Molecular Dynamics Study of the Binary Complexes of APP, JIP1, and the Cargo Binding Domain of KLC. Proteins 2017, 85 (2), 221–234. https://doi.org/10.1002/prot.25208.
  16. Miller, B. R.; Beese, L. S.; Parish, C. A.; Wu, E. Y. The Closing Mechanism of DNA Polymerase I at Atomic Resolution. Structure 2015, 23 (9), 1609–1620. https://doi.org/10.1016/j.str.2015.06.016.
  17. Miller, B. R.; Parish, C. A.; Wu, E. Y. Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I. PLoS Comput. Biol. 2014, 10 (12), e1003961. https://doi.org/10.1371/journal.pcbi.1003961.
  18. Wu, E. Y.; Walsh, A. R.; Materne, E. C.; Hiltner, E. P.; Zielinski, B.; Miller, B. R.; Mawby, L.; Modeste, E.; Parish, C. A.; Barnes, W. M.; Kermekchiev, M. B. A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase. Biochemistry 2015, 54 (3), 881–889. https://doi.org/10.1021/bi501198f.
  19. Miller, B. R.; Roitberg, A. E. Trypanosoma Cruzi Trans-Sialidase as a Drug Target against Chagas Disease (American Trypanosomiasis). Future Med. Chem. 2013, 5 (15), 1889–1900. https://doi.org/10.4155/fmc.13.129.
  20. Miller, B. R.; Roitberg, A. E. Design of E-Pharmacophore Models Using Compound Fragments for the Trans-Sialidase of Trypanosoma Cruzi: Screening for Novel Inhibitor Scaffolds. J. Mol. Graph. Model. 2013, 45, 84–97. https://doi.org/10.1016/j.jmgm.2013.08.009.
  21. Miller, B. R.; McGee, T. D.; Swails, J. M.; Homeyer, N.; Gohlke, H.; Roitberg, A. E. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. J. Chem. Theory Comput. 2012, 8 (9), 3314–3321. https://doi.org/10.1021/ct300418h.
  22. Roberts, B. P.; Miller, B. R. I.; Roitberg, A. E.; Merz, K. M. Jr. Wide-Open Flaps Are Key to Urease Activity. J. Am. Chem. Soc. 2012, 134 (24), 9934–9937. https://doi.org/10.1021/ja3043239.
  23. Michael, L. A.; Chenault, J. A.; Miller, B. R.; Knolhoff, A. M.; Nagan, M. C. Water, Shape Recognition, Salt Bridges, and Cation-Pi Interactions Differentiate Peptide Recognition of the HIV Rev-Responsive Element. J. Mol. Biol. 2009, 392 (3), 774–786. https://doi.org/10.1016/j.jmb.2009.07.047.