MacroModel References

1.

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2.

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3.

Allinger, N. L.; Yuh, Y. H.; Lii, J-HMolecular Mechanics. The MM3 Force Field for Hydrocarbons. 1. J. Am. Chem. Soc. 1989, 111, 8551.

4.

Weiner, S. J.; Kollman, P.; Case, D.; Singh, U.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. A new Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins. J. Am. Chem. Soc. 1984, 106, 765.

5.

Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 1986, 7, 230.

6.

Ferguson, D. M.; Kollman, P. A. Can the Lennard-Jones 6-12 function replace the 10-12 form in molecular mechanics calculations? J. Comput. Chem. 1991, 12, 620.

7.

McDonald, D. Q.; Still, W. C. AMBER torsional parameters for the peptide backbone. Tetrahedron Lett. 1992, 33, 7743.

8.

Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179.

9.

Jorgensen, W. L.; Tirado-Rives, J. The OPLS Potential Functions for Proteins. Energy Minimization for Crystals of Cyclic Peptides and Crambin. J. Am. Chem. Soc. 1988, 110, 1657.

10.

Halgren, T. A. Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization and Performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.

11.

Halgren, T. A. Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions. J. Comput. Chem. 1996, 17, 520-552.

12.

Halgren, T. A. Merck Molecular Force Field. III. Molecular Geometrics and Vibrational Frequencies for MMFF94. J. Comput. Chem. 1996, 17, 553-586.

13.

Halgren, T. A.; Nachbar, R. B. Merck Molecular Force Field. IV. Conformational Energies and Geometries. J. Comput. Chem. 1996, 17, 587-615.

14.

Halgren, T. A. Merck Molecular Force Field. V. Extension of MMFF94 using Experimental Data, Additional Computational Data and Empirical Rules. J. Comput. Chem. 1996, 17, 616-641.

15.

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16.

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17.

Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am Chem. Soc. 1996, 118, 11225-11236.

18.

Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides. J. Phys. Chem. B 2001, 105, 6474-6487.

19.

Hasel, W.; Hendrickson, T. F.; Still, W. C. A Rapid Approximation to the Solvent Accessible Surface Areas of Atoms. Tetrahedron Comput. Methodol. 1988, 1, 103.

20.

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21.

Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 112, 6127.

22.

Cheng, A.; Best, S. A.; Merz, K. M. Jr.; Reynolds, C. H. GB/SA water model for the Merck molecular force field (MMFF). J. Mol. Graphics Modell. 2000, 18, 273–282.

23.

Best, S. A.; Merz, K. M., Jr.; Reynolds, C. H. A GB/SA Based Continuum Solvation Model for Octanol. J. Phys. Chem. B 1997, 101, 10479-10487.

24.

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25.

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26.

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27.

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28.

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29.

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30.

Kolossváry, I.; Guida, W. C. Low Mode Search. An efficient, automated computational method for conformational analysis: application to cyclic and acyclic alkanes and cyclic peptides. J. Am. Chem. Soc. 1996, 118, 5011.

31.

Kolossváry, I.; Guida, W. C. Low-mode Conformational Search Elucidated. Application to C39H80 and Flexible Docking of 9-Deazaguanine Inhibitors to PNP. J. Comp. Chem. 1999, 20, 1671.

32.

Kolossváry, I.; Keseru, G. M. Hessian-Free Low-Mode Conformational Search for Large-Scale Protein Loop Optimization: Application to c-jun N-Terminal Kinase JNK3. J. Comput. Chem. 2001, 22, 21.

33.

Keseru, G. M.; Kolossváry, I. Fully Flexible Low-Mode Docking: Application to Induced Fit in HIV Integrase. J. Am. Chem. Soc. 2001, 123, 12708.

34.

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35.

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36.

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37.

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38.

Chang, G.; Guida, W. C.; Still, W. C. An internal coordinate Monte-Carlo method for searching conformational space. J. Am. Chem. Soc. 1989, 111, 4379.

39.

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40.

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41.

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42.

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43.

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44.

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45.

van Gunsteren, W. F.; Berendsen H. J. C. A leap-frog algorithm for stochastic dynamics. Mol. Simul. 1988, 1, 173.

46.

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47.

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48.

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49.

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50.

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51.

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52.

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53.

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54.

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55.

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56.

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57.

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58.

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59.

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61.

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62.

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63.

Roos, K.; Wu, C.; Damm, W.; Reboul, M.; Stevenson, J. M.; Lu, C.; Dahlgren, M. K.; Mondal, S.; Chen, W.; Wang, L.; Abel, R.; Friesner, R. A.; Harder, E. D. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. J. Chem. Theory Comput., 2019, 15, 1863. DOI: 10.1021/acs.jctc.8b01026