By Arthur K. Cho, Terrence F. Blaschke, Paul A. Insel, Horace H. Loh
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Additional info for Annual Review of Pharmacology and Toxicology: 2003
58–60) developed dynamic pharmacophore models that perform better than the single conformation model in identifying potent inhibitors of HIV-1 integrase. Unfortunately, the dynamic model also increased the number of false positives. Relaxed Complex Methods Recently, another computational approach has been described to discover ligands that may bind with “induced fit” of their target molecules (62, 62a). The new methods, which are called “relaxed complex methods,” are inspired by two successful experimental methods for rapid discovery of ligands that bind strongly to a receptor, namely the “SAR by NMR” method (63) and the “tether method” (64).
1992. Locally enhanced sampling in free energy calculations—application of mean field approximation to accurate calculation of free energy differences. J. Chem. Phys. 97:7838 11. Elber R, Karplus M. 1990. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monox- 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. ide diffusion through myoglobin. J. Am. Chem. Soc. 112:9161–75 Simmerling C, Fox T, Kollman PA. 1998. Use of locally enhanced sampling in free energy calculations: testing and application to the alpha → beta anomerization of glucose.
Estimating the relative free energy of different molecular states with respect to a single reference state. J. Phys. Chem. 100:9485–94 Mordasini TZ, McCammon JA. 2000. Calculations of relative hydration free energies: a comparative study using thermodynamic integration and an extrapolation method based on a single reference state. J. Phys. Chem. B 104:360–67 Vorobjev YN, Almagro JC, Hermans J. 1998. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.
Annual Review of Pharmacology and Toxicology: 2003 by Arthur K. Cho, Terrence F. Blaschke, Paul A. Insel, Horace H. Loh