Publications by the Conifer Point team related to fragment-based design1-10

  1. Guarnieri F, Kulp JL Jr, Kulp JL III, Cloudsdale IS, Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations. PLoS ONE 2019, 14(12): e0225780.
  2. Cloudsdale, I. S.; Dickson, J. K., Jr.; Barta, T. E.; Grella, B. S.; Smith, E. D.; Kulp, J. L., 3rd; Guarnieri, F.; Kulp, J. L., Jr., Design, synthesis and biological evaluation of renin inhibitors guided by simulated annealing of chemical potential simulations. Bioorganic & Medicinal Chemistry 2017, 25 (15), 3947-3963.
  3. Kulp, J. L., 3rd; Cloudsdale, I. S.; Kulp, J. L., Jr.; Guarnieri, F., Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition. PLoS ONE 2017, 12 (8), e0183327.
  4. Guarnieri, F., Designing an orally available nontoxic p38 inhibitor with a fragment-based strategy. Methods in Molecular Biology 2015, 1289, 211-26.
  5. Guarnieri, F., Designing a small molecule erythropoietin mimetic. Methods in Molecular Biology 2015, 1289, 185-210.
  6. Boyer, R. D.; Bryan, R. L., Fast estimation of solvation free energies for diverse chemical species. The Journal of Physical Chemistry B 2012, 116 (12), 3772-9.
  7. Kulp III, J. L.; Blumenthal, S. N.; Wang, Q.; Guarnieri, F., A Fragment-based Approach to the SAMPL3 Challenge. Journal of Computer-Aided Molecular Design 2012, 583-94.
  8. Moffett, K.; Konteatis, Z.; Nguyen, D.; Shetty, R.; Ludington, J.; Fujimoto, T.; Lee, K. J.; Chai, X.; Namboodiri, H.; Karpusas, M.; Dorsey, B.; Guarnieri, F.; Bukhtiyarova, M.; Springman, E.; Michelotti, E., Discovery of a novel class of non-ATP site DFG-out state p38 inhibitors utilizing computationally assisted virtual fragment-based drug design (vFBDD). Bioorganic & Medicinal Chemistry Letters 2011, 21 (23), 7155-65.
  9. Kulp III, J. L.; Kulp Jr, J. L.; Pompliano, D. L.; Guarnieri, F., Diverse fragment clustering and water exclusion identify protein hot spots. Journal of the American Chemical Society 2011, 133 (28), 10740-3.
  10. Clark, M.; Guarnieri, F.; Shkurko, I.; Wiseman, J., Grand Canonical Monte Carlo Simulation of Ligand−Protein Binding. Journal of Chemical Information and Modeling 2006, 46 (1), 231-242.
  11. Guarnieri, F.; Mezei, M., Simulated Annealing of Chemical Potential:  A General Procedure for Locating Bound Waters. Application to the Study of the Differential Hydration Propensities of the Major and Minor Grooves of DNA. Journal of the American Chemical Society 1996, 118 (35), 8493-8494.