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Original Articles

Conformational Space Comparison of GnRH and lGnRH-III using Molecular Dynamics, Cluster Analysis and Monte Carlo Thermodynamic Integration

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Pages 733-748 | Received 24 Aug 2000, Published online: 15 May 2012

References and footnotes

  • Lovas , S. , Pályi , I. , Vincze , B. , Horváth , J. , Kovács , M. , Mezö , I. , Tóth , G. , Teplán , I. and Murphy , R. F. 1998 . J. Pept. Res. , 52 : 384 – 389 .
  • Sealfon , S. C. , Weinstein , H. and Millar , R. P. 1997 . R.P. Endocrine Rev. , 18 : 180 – 205 .
  • Mezö , I. , Lovas , S. , Pályi , I. , Vincze , B. , Kálnay , A. , G. Turi , Z. Vadász , J. Seprödi , M. Idei , Tóth , G. , Gulyás , E. , Ötvös , F. , Mák , M. , Horváth , J. , Teplán , I. and Murphy , R. F. 1997 . J. Med. Chem. , 40 : 3353 – 3358 .
  • Bayly , C. I. , Cieplak , P. , Cornell , W. D. and Kollman , P. A. 1993 . J. Phys. Chem. , 97 : 10269 – 10280 .
  • Cornell , W. D. , Cieplak , P. , Bayly , C. I. and Kollman , P. A. 1993 . J. Am. Chem. Soc. , 115 : 9620 – 9631 .
  • Cornell , W. D. , Cieplak , P. , Bayly , C. I. , Gould , I. R. , Merz , K. Jr. , Ferguson , D. M. , Spellmeyer , D. C. , Fox , T. , Caldwell , J. W. and Kollman , P. A. 1995 . J. Am. Chem. Soc. , 117 : 5179 – 5197 .
  • Cieplak , P. , Cornell , W. D. , Bayly , C. I. and Kollman , P. A. 1995 . J. Comp. Chem. , 16 : 1357 – 1377 .
  • 1996 . Tripos Inc. Sybyl version 6.4 Users Manual St. Louis : Tripos Inc. .
  • Case , D. A. , Pearlman , D. A. , Caldwell , J. W. , Cheatham , T. E. III , Ross , W. S. , Simmerling , C. , Darden , T. , Merz , K. M. , Stanton , R. V. , Cheng , A. , Vincent , J. J. , Crowley , M. , Ferguson , D. M. , Radmer , R. , Seibel , G. L. , Singh , U. C. , Weiner , P. and Kollman , P. A. 1997 . AMBER version 5.0. San Francisco : University of California .
  • Pearlman , D. A. , Case , D. A. , Caldwell , J. W. , Ross , W. S. , Cheatham , T. E. III , DeBolt , S. , Ferguson , D. M. , Seibel , G. and Kollman , P. A. 1995 . Comp. Phys. Commun. , 91 : 1 – 41 .
  • Schmidt , M. W. , Baldridge , K. K. , Boatz , J. A. , Elbert , S. T. , Gordon , M. S. , Jensen , J. H. , Koseki , S. , Matsunaga , N. , Nguyen , K. A. , Su , S. J. , Windus , T. L. , Dupuis , M. and Montgomery , J. A. 1993 . J. Comp. Chem. , 14 : 1347 – 1363 .
  • Still , W. C. , Tempczyk , A. , Hawley , R. C. and Hendrickson , T. 1990 . J. Am. Chem. Soc. , 112 : 6127 – 6129 .
  • Berendsen , H. J.C. , Postma , J. P.M. , van Gunsteren , W. F. , DiNola , A. and Haak , J. R. 1984 . J. Chem. Phys. , 81 : 3684 – 3690 .
  • Allen , M. P. and Tildesley , D. J. 1987 . Computer Simulation of Liquids New York : Oxford University Press .
  • Ponder , J. W. 1997 . “ Tinker User's Manual ” . In Washington University School of Medicine. St. Louis http://dasher.wustl.edu
  • Lovas , S. and Murphy , R. F. 1997 . Molecular Modeling of Neuropeptides. , 73 : 209 – 217 .
  • Jorgensen , W. L. , Chaudreskhar , J. , Madura , J. D. , Impey , R. W. and Klein , M. L. 1982 . J. Chem. Phys. , 79 : 926 – 935 .
  • Kaufman , L. and Rousseeuw , P. J. 1990 . Finding Groups in Data: An Introduction to Cluster Analysis New York : John Wiley & Sons, Inc. .
  • Watts , C. R. , Tóth , G. , Murphy , R. F. and Lovas , S. 2001 . J. Mol. Struct. (THEOCHEM) , 535 : 171 – 182 .
  • Kabsch , W. and Sander , C. 1983 . Biopolymers , 22 : 2577 – 2637 .
  • van derSpoel , D. , van Bunren , A. R. , Apol , E. , Meulenhoff , P. J. , Tielman , D. P. , Sijbers , A. L.T.M. , Hess , B. , Feenstra , K. A. , Lindahl , E. , van Drunen , R. and Berendsen , H. J.C. 1999 . GROMACS version 2.0 Users Manual. The Netherlands : Groningen . http://md.chem.rug.nl/∼gmx
  • Burley , C. A. and Petsko , G. A. 1985 . Science , 229 : 23 – 29 .
  • Mezei , M. and Beveridge , D. L. 1986 . Ann. Acad. Sci. N.Y. , 482 : 1 – 23 .
  • Mezei , M. 1992 . M.J. Comp. Chem. , 13 : 651 – 656 .
  • Mezei , M. and Guarnieri , F. 1998 . J. Biomol. Struct. Dyn. , 16 : 723 – 732 .
  • Mezei , M. 2000 . MMC. New York : Molecular Monte Carlo User's Guide, Mount Sinai School of Medicine . http://inka.mssm.edu/∼mezei/mmc
  • Mezei , M. 1997 . J. Comp. Chem. , 18 : 812 – 815 .
  • Mezei , M. and Simulaid . 2000 . Simulation Setup Utilities. New York : Mount Sinai School of Medicine . http://inka.mssm.edu/∼mezei/simulaid
  • Zimmerman , S. S. , Pottle , M. S. , Nemethy , G. and Scheraga , H. A. 1977 . Macromolecules , 10 : 1 – 9 .
  • Nagy , P. I. , Bitar , J. E. and Smith , D. E. 1994 . J. Comp. Chem. , 15 : 1228 – 1240 .

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