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MacroModel Reference Manual - ISP

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<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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