Publications of Jonathan W. Greene

(Chemistry-Related)

(See here for engineering-related publications.)

  1. P. Shenkin, J. Greene,
    "Can Rotamer Libraries be Used to Predict Sidechain Conformation in Globular Proteins?
    " AAAS Ann. Mtg, 1989.
  2. H. Farid, P. Shenkin, J. Greene, J. Fetrow,
    "Prediction of Sidechain Conformations in Protein Cores and Loops from Rotamer Libraries
    ," Biophysics Society Conference, Houston, TX, Feb. 1992.
  3. P. Sprague, J. Greene, S. Teig.
    "Application of Hypothesis Generation Tools to ACE and PAF Drug Discovery Problems
    ," Amer. Chem. Soc. Nat'l Mtg., April 1992.
  4. J. Greene, S. Teig,
    "Catalyst: Generating and Testing Chemical Hypotheses for Structure Activity
    ," Amer. Chem. Soc. Nat'l Mtg., April 1992.
  5. S. Kahn, S. Berezin, J. Greene, S. Ku,
    "Integrated 1d, 2d and 3d Queries in the Drug Design Process
    ," 12th Ann. Conf. Molecular Graphics Soc., Interlaken, June 1993.
  6. S. Berezin, J. Greene, S. Kahn, S. Ku, S. Teig,
    "CHM: A New Chemically Expressive Database Query Language
    ," Noordwijkerhout Camarino Med. Chem. Symp., Netherlands, June 1993.
  7. J. Greene,
    "Statistical Analysis of Structure-Activity Hypotheses
    ," Invited talk, Gordon Research Conf. on QSAR, August 1993.
  8. J. Greene, S. Kahn, P. Sprague, S. Teig,
    "Molecular Similarity
    ," Amer. Chem. Soc. Nat'l Mtg., March 1994.
  9. S. Kahn, J. Greene, A. Smellie, S. Teig.
    "Drug Discovery Using Database Searching: The Problems of False Negatives and False Positive
    ," Nat'l Chem. Inf. Symp., Burlington, VT, June 1994.
  10. J. Greene, S. Kahn, H. Savoj, P. Sprague, S. Teig,
    "Chemical Function Queries for 3D Database Search
    ," J. Chem. Info. Comput. Sci., 1994, 34, 1297-1308. [pdf]
  11. J. Greene, A. Smellie, S. Teig,
    "Selection of Informative Screening Libraries
    ," Amer. Chem. Soc. Nat'l Mtg., April 1995.
  12. J. Greene, D. Barnum, S. Teig,
    "Diversity, Shmiversity... is Your Library Any Good?
    " Exploiting Molecular Diversity, Cambridge Healthtech Inst., Coronado, CA, Jan. 1996.
  13. J. Greene, D. Barnum, S. Teig.
    "Evaluating Compound Libraries for Structure-Activity Information Content
    ," IBC Conf. on Peptidomimetics and Small Molecule Design, Washington, DC, March 1996.
  14. P. Myers, J. Greene, J. Saunders, S. Teig,
    "Rapid, Reliable Drug Discovery
    ," Today's Chemist at Work, 1997, 6, 45-53.
  15. J. Saunders, P. Myers, D. Barnum, J. Greene, S. Teig,
    "Drug Discover Development of a Univeral Informer Library: Data Derived from the Training Set
    ," Genetic Engineering News, Nov. 15, 1997, 17:20. [pdf]
  16. P. Beroza, E. Bradley, J. Eksterowicz, R. Feinstein, J. Greene, P. Grootenhuis, R. Henne, J. Mount, W. Shirley, A. Smellie, R. Stanton, D. Spellmeyer,
    "Application of Random Sampling to Virtual Screening of Combinatorial Libraries
    ," J. Molecular Graphics and Modelling., 2000, 18, 335-342. [pdf]
  17. S. Putta, C. Lemmen, P. Beroza, J. Greene,
    "A Novel Shape-Feature Based Approach to Virtual Screening
    ," J. Chem. Inf. Comput. Sci. 2002, 42, 1230-1240. [pdf]
  18. J. Greene,
    "Facilitating Virtual Screening Flows with Python
    ," Proc. of the CHI Conf. Intelligent Drug Discovery & Development, Cambridge Healthtech Inst., Cambridge, MA, 2002.
  19. H. Claußen, M. Gastreich, V. Apelt, J. Greene, S.A. Hindle, and C. Lemmen,
    "FlexX Goes SQL - Automated Pharmacophore Generation
    ," Amer. Chem. Soc. Nat'l Mtg., Sept., 2003. [pdf]
  20. J. Lanctot, S. Putta, C. Lemmen, J. Greene,
    "Using Ensembles to Classify Compounds for Drug Discovery
    ," J. Chem. Inf. Comput. Sci., 2003, 43, 2163-2169. [pdf]
  21. T. Shiota, S. Yamagami, K. Kataoka, N. Endo, H. Tanaka, D. Barnum, J. Greene, W. Moree, M. Weinhouse, C. Tarby,
    "Diarylalkyl Cyclic Diamine Derivatives as Chemokine Receptor Antagonists
    ," U.S. Patent 6,686,353, February 3, 2004.
  22. H. Claußen, M. Gastreich, V. Apelt, J. Greene, S. Hindle, and C. Lemmen,
    "The FlexX Database Docking Environment - Rational Extraction of Receptor Based Pharmacophores
    ," Current Drug Discovery Technologies, 2004, 1, 49-60. [pdf]
  23. M. Imai, T. Shiota, K. Kataoka, C. Tarby, W. Moree, T. Tsutsumi, M. Sudo, M. Ramirez-Weinhouse, D. Comer, C. Sun, S. Yamagami, H. Tanaka, T. Morita, T. Hada, J. Greene, D. Barnum, J. Saunders, P. Myers, Y. Kato, N. Endo,
    "Small molecules inhibitors of the CCR2b receptor. Part 1: Discovery and optimization of homopiperazine derivatives
    ," Bioorganic & Medicinal Chemistry Letters, 2004, 14, 5407-5411.
  24. W. Moree, K. Kataoka, M. Ramirez-Weinhouse, T. Shiota, M. Imai, M. Sudo, T. Tsutsumi, N. Endo, Y. Muroga, T. Hada, H. Tanaka, T. Morita, J. Greene, D. Barnum, J. Saunders, Y. Kato, P. Myers, C. Tarby
    "Small molecule antagonists of the CCR2b receptor. Part 2: Discovery process and initial structure-activity relationships of diamine derivatives
    ," Bioorganic & Medicinal Chemistry Letters, 2004, 14, 5413 - 5416.