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Conformational energy downward driver (CEDD): Characterization and calibration of the method

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Summary

A method has been developed that allows one to drive a molecule to conformations of lowest energy given the starting conformation, the identity of the rotatable bonds and the step size. This method has proved useful in our hands in the drug design arena where it is frequently more important to get ‘low-energy’ conformers of a molecule that match some other (e.g. pharmacophoric or enzyme pocket) requirements than to exhaustively enumerate all possible low-energy conformations for each of the molecules to be studied. The method has been shown to work in the test cases studied to date. Furthermore, so far it has been shown to be sufficiently fast to be used for molecules containing up to 70 rotatable bonds.

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References

  1. Barton, D.H.R., J. Chem. Soc., (1953) 1027.

  2. Ghose, A.K., Jaeger, E.P., Kowalczyk, P.J., Peterson, M.L. and Treasurywala, A.M., J. Comput. Chem., 14 (1993) 1050, and references cited therein.

    Google Scholar 

  3. Viswanathan, V.N., Ghose, A.K., Revanker, G.R. and Robins, R.K., J. Chem. Inf. Comput. Sci., 29 (1989) 163.

    Google Scholar 

  4. SYBYL, Version 5.5, Tripos Associates, St. Louis, MO.

  5. This set of molecules has been used as a test set for the validation of several force fields and is the subject of a systematic analysis of conformational analysis methods in our laboratories. See Ref. 1 above and references cited therein.

  6. Dewar, M.J.S., Zoebisch, E.G., Healy, E.F. and Stewart, J.J.P., J. Am. Chem. Soc., 107 (1985) 3902.

    Google Scholar 

  7. Dewar, M.J.S. and Yuan, Y.C., Inorg. Chem., 29 (1990) 3881.

    Google Scholar 

  8. Saunders, M., J. Am. Chem. Soc., 109 (1987) 3150.

    Google Scholar 

  9. Saunders, M., J. Comput. Chem., 12 (1991) 645.

    Google Scholar 

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Authors and Affiliations

  1. Biophysics and Computational Chemistry, Sterling Winthrop Inc., P.O. Box 5000, 19426-0900, Collegeville, PA, U.S.A.

    E. P. Jaeger, M. L. Peterson & A. M. Treasurywala

Authors
  1. E. P. Jaeger
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  2. M. L. Peterson
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  3. A. M. Treasurywala
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Jaeger, E.P., Peterson, M.L. & Treasurywala, A.M. Conformational energy downward driver (CEDD): Characterization and calibration of the method. J Computer-Aided Mol Des 9, 55–64 (1995). https://doi.org/10.1007/BF00117278

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  • DOI: https://doi.org/10.1007/BF00117278

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