Publications

Publications

  1. Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors. Jacob D. Durrant and J. Andrew McCammon. 2011. BMC Pharmacology. 11: 9.
  2. HBonanza: A Computer Algorithm for Molecular-Dynamics-Trajectory Hydrogen-Bond Analysis. Jacob D. Durrant and J. Andrew McCammon. 2011. Journal of Molecular Graphics and Modelling. 31: 5-9.
  3. Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design. Jacob D. Durrant, Rong Cao, Alemayehu A. Gorfe, Wei Zhu, Jikun Li, Anna Sankovsky, Eric Oldfield, and J. Andrew McCammon. 2011. Computational Biology & Drug Design. 78(3):323-332.
  4. Pyrone-Based Inhibitors of Metalloproteinases Types 2 and 3 May Work as Conformation-Selective Inhibitors. Jacob D. Durrant, César de Oliveira, and J. Andrew McCammon. 2011. Computational Biology & Drug Design. 78(2):191-198. Article featured on cover.
  5. BINANA: A Novel Algorithm for Ligand-Binding Characterization. Jacob D. Durrant and J. Andrew McCammon. 2011. Journal of Molecular Graphics and Modelling. doi:10.1016/j.jmgm.2011.01.004
  6. POVME: An Algorithm for Measuring Binding-Pocket Volumes. Jacob D. Durrant, César Augusto F. de Oliveira, and J. Andrew McCammon. 2010. Journal of Molecular Graphics and Modelling. doi:10.1016/j.jmgm.2010.10.007
  7. Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target. William Sinko, César de Oliveira, Sara Williams, Adam Van Wynsberghe, Jacob D. Durrant, J. Andrew McCammon. Chemical Biology & Drug Design. doi:10.1111/j.1747-0285.2011.01101.x
  8. Computer-Aided Drug-Discovery Techniques that Account for Receptor Flexibility. Jacob D. Durrant and J. Andrew McCammon. 2010. Current Opinion in Pharmacology. 2010. Current Opinion in Pharmacology. 10(6):770-774.
  9. NNScore: A Neural Network Based Scoring Function for the Characterization of Protein-Ligand Complexes. Jacob D. Durrant; J. Andrew McCammon. 2010. Journal of Chemical Information and Modeling, 50(10): 1865-1871.
  10. Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1. Jacob D. Durrant, Laurence Hall, Robert V. Swift, Melissa Landon, Achim Schnaufer, Rommie E. Amaro. 2010. PLoS Negl Trop Dis. 24;4(8). pii: e803.
  11. Computer-Aided Identification of Trypanosoma brucei Uridine Diphosphate Galactose 4'-Epimerase Inhibitors: Towards the Development of Novel Therapies for African Sleeping Sickness. Jacob D. Durrant; Michael D. Urbaniak; Michael A. J. Ferguson; J. Andrew McCammon. 2010. Journal of Medicinal Chemistry, 53(13): 5025–5032.
  12. Potential Drug-Like Inhibitors of Group 1 Influenza Neuraminidase Identified through Computer-Aided Drug Design. Jacob D. Durrant; J. Andrew McCammon. 2010. Computational Biology and Chemistry 34:97-105.
  13. Computational Identification of Uncharacterized Cruzain Binding Sites. Jacob D. Durrant; Henrik Keränen; Benjamin Wilson; J. Andrew McCammon. 2010. PLoS Neglected Tropical Diseases 4(5):e676.
  14. A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. Jacob D. Durrant; Rommie E. Amaro; Lei Xie; Michael D. Urbaniak; Michael A. J. Ferguson; Antti Haapalainen; Zhijun Chen; Anne Marie Di Guilmi; Frank Wunder; Philip E. Bourne; J. Andrew McCammon. 2010. PLoS Comp. Bio., 6(1):e1000648.
  15. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J. Durrant; C. A. F. Oliveira; J. A. McCammon. 2010. J. Mol. Recognition, 23(2):173–182.
  16. Toward Understanding the Conformational Dynamics of RNA Ligation. Swift, R. V.; Durrant, J.; Amaro, R. E.; McCammon, J. A. 2009. Biochemistry, 48(4):709–19.
  17. AutoGrow: A Novel Algorithm for Protein Inhibitor Design. Durrant, J. D.; Amaro, R. E.; McCammon, J. A. 2009. Chemical Biology & Drug Design. 73(2):168-78.
  18. Tryptophan contributions to the empirical free-energy profile in gramicidin A/M heterodimer channels. Durrant, J. D.; Caywood, D.; Busath, D. D. 2006. Biophys J. 1;91(9):3230-41.
  19. An algorithm for analyzing linkages affected by heterozygous translocations: QuadMap. Durrant, J. D.; Gardunia, B. W., Livingstone, K. D., Stevens, M. R., Jellen, E. N. 2006. Journal of Heredity 97:62-66.
  20. Modulation of Lipid Bilayer Interfacial Dipole Potential by Phloretin, RH421, and 6-Ketocholestanol as Probed by Gramicidin Channel Conductance. Duffin, R. L; Garrett, M. P.; Flake, K. B.; Durrant, J. D.; Busath, D. D.; Langmuir; 2003; 19(8); 3561-3561.
  21. Segregation Patterns in Oat Populations Derived From Parents Heterozygous for Translocations 7C-17 and 6C-21. Eric N. Jellen, Brian W. Gardunia, Jacob Durrant, F. Douglas Raymond, J. Paul Murphy, David P. Livingston, and Albert G. Santos. 2002. American Oat Workers Conference Proceedings.