<strong>Reference</strong>s12. Halgren, T. A. Merck Molecular Force Field. V. Extension of MMFF94 using ExperimentalData, Additional Computational Data and Empirical Rules. J. Comput. Chem.1996, 17, 616-641.13. Halgren, T. A. MMFF VI. MMFF94s Option for Energy Minimization Studies. J.Comput. Chem. 1999, 20, 720-729.14. Halgren, T. A. MMFF VII. Characterization of MMFF94, MMFF94s and Other WidelyAvailable Force Fields for Conformational Energies and for Intermolecular InteractionEnergies and Geometries. J. Comput. Chem. 1999, 20, 730-748.15. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of theOPLS All-Atom Force Field on Conformational Energetics and Properties of OrganicLiquids. J. Am Chem. Soc. 1996, 118, 11225-11236.16. Hasel, W.; Hendrickson, T. F.; Still, W. C. A Rapid Approximation to the SolventAccessible Surface Areas of Atoms. Tetrahedron Comput. Methodol. 1988, 1, 103.17. Ooi, T.; Oobatake, M.; Nemethy, G.; Scheraga, H. A. Accessible Surface Areas as aMeasure of the Thermodynamic Parameters of Hydration of Peptides. PNAS 1987, 84,3086.18. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical treatment ofsolvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 112, 6127.19. Cheng, A.; Best, S. A.; Merz, K. M. Jr.; Reynolds, C. H. GB/SA water model for theMerck molecular force field (MMFF). J. Mol. Graphics Modell. 2000, 18, 273–282.20. Best, S. A.; Merz, K. M., Jr.; Reynolds, C. H. A GB/SA Based Continuum SolvationModel for Octanol. J. Phys. Chem. B 1997, 101, 10479-10487.21. Hay, B. P. Methods for molecular mechanics modeling of coordination compounds.Coord. Chem. Rev. 1993, 126, 177-236.22. Polak, E.; Ribiere, G. Note sur la Convergence de Methodes de Directions Conjuguees.Revue Francaise Inf. Rech. Oper., Serie Rouge 1969, 16-R1, 35.23. Oren, S. S.; Spedicato, E. Optimal conditioning of self-scaling variable metric algorithms.Mathematical Programming. Math. Programming 1976, 10, 70.24. Ponder, J. W.; Richards, F. M. An Efficient Newton-like Method for MolecularMechanics Energy Minimization of Large Molecules. J. Comput. Chem. 1987, 8, 1016.25. Culot, P.; Dive, G.; Nguyen, V. H.; Ghuysen, J. M. A Quasi-Newton Algorithm forFirstOrder Saddle Point Location. Theor. Chim. Acta 1992, 82, 189.238<strong>MacroModel</strong> 9.7 <strong>Reference</strong> <strong>Manual</strong>
<strong>Reference</strong>s26. Sefler, A. M.; Lauri, G.; Bartlett, P. A. A Convenient Method for Determining CyclicPeptide Conformation from 1D 1H-NMR Information. Int. J. Pept. Protein Res. 1996,48, 129.27. Kolossváry, I.; Guida, W. C. Low Mode Search. An efficient, automated computationalmethod for conformational analysis: application to cyclic and acyclic alkanes and cyclicpeptides. J. Am. Chem. Soc. 1996, 118, 5011.28. Kolossváry, I.; Guida, W. C. Low-mode Conformational Search Elucidated. Applicationto C39H80 and Flexible Docking of 9-Deazaguanine Inhibitors to PNP. J. Comp. Chem.1999, 20, 1671.29. Kolossváry, I.; Keseru, G. M. Hessian-Free Low-Mode Conformational Search forLarge-Scale Protein Loop Optimization: Application to c-jun N-Terminal Kinase JNK3.J. Comput. Chem. 2001, 22, 21.30. Keseru, G. M.; Kolossváry, I. Fully Flexible Low-Mode Docking: Application toInduced Fit in HIV Integrase. J. Am. Chem. Soc. 2001, 123, 12708.31. Shenkin, P. S.; Yarmush, D. L.; Fine, R. M.; Wang, H.; Levinthal, C. Predicting antibodyhypervariable loop conformation. I. Ensembles of random conformations for ringlikestructures. Biopolymers 1987, 26, 2053-2085.32. Fine, R. M.; Wang, H.; Shenkin, P. S.; Yarmush, D. L.; Levinthal, C. Predicting AntibodyHypervariable Loop Conformations. II: Minimization And Molecular DynamicsStudies Of MCPC603 From Many Randomly Generated Loop Conformations. Proteins1986, 1, 342.33. Sorensen, D. C. ARPACK Tutorial: Implicitly Restarted Arnoldi/Lanczos Methods forLarge Scale Eigenvalue Calculations; Rice University: Houston, TX, 1995.34. Lehoucq, R. B.; Sorensen, D. C.; Yang, C. ARPACK User’s Guide: Solution of LargeScale Eigenvalue Problems With Implicitly Restarted Arnoldi Methods; Rice University:Houston, TX, 1997.35. Chang, G.; Guida, W. C.; Still, W. C. An internal coordinate Monte-Carlo method forsearching conformational space. J. Am. Chem. Soc. 1989, 111, 4379.36. Saunders, M.; Houk, K. N.; Wu, Y.-D.; Still, C. W.; Lipton, M.; Chang, G.; Guida, W. C.Conformations of Cycloheptadecane: A Comparison of Methods for ConformationalSearching. J. Am. Chem. Soc. 1990, 112, 1419.37. Goodman, J. M.; Still, W. C. Searching Conformation Space. J. Comput. Chem. 1991,12, 1110.38. Li, Z.; Scheraga. H. Monte Carlo-minimization approach to the multiple-minimaproblem in protein folding. PNAS 1987, 84, 6611.<strong>MacroModel</strong> 9.7 <strong>Reference</strong> <strong>Manual</strong> 239
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