Desmond References

1. Bowers, K.J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregerson, B. A.; Klepeis, J. L.; Kolossvary, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters, Proceedings of the ACM/IEEE Conference on Supercomputing(SC06), Tampa, Florida, November 11-17, 2006, http://sc06.supercomputing.org/schedule/event_detail.php?evid=9088.
2. Shaw, D.E. A fast, scalable method for the parallel evaluation of distance-limited pair wise particle interactions. J. Comput. Chem. 2005, 26, 1318.
3. Bowers, K.J.; Dror, R.O.; Shaw, D.E. The midpoint method for parallelization of particle simulations. J. Chem. Phys. 2006, 124, 184109.
4. Bowers, K.J.; Dror, R.O.; Shaw, D.E. Zonal methods for the parallel execution of range-limited N-body simulations. J. Comput. Phys. 2007, 221, 303.
5. Lippert, R.A.; Bowers, K.J.; Dror, R. O.; Eastwood, M.P.; Gregersen, B. A.; Klepeis, J. L.; Kolossvary, I.; Shaw, D. E. A common, avoidable source of error in molecular dynamics integrators. J. Chem. Phys. 2007, 126, 046101.
6. Arkin, I.T.; et al. Mechanism of Na+/H+ Antiporting. Science, 2007, 317, 799.
7. Humphrey, W.; Dalke, A.; Schulten, K. VMD - Visual Molecular Dynamics, J. Molec. Graphics, 1996, 14, 33.
8. Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan Y.; Wriggers, W. Science 2010, 330, 341.
9. Piana, S.; Lindorff-Larsen, K.; Shaw, D. E. How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization? Biophys. J. 2011, 100, L47.
10. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J., J. Am Chem. Soc. 1996, 118, 11225.
11. Damm, W.; Frontera, A.; Tirado-Rives, J.; Jorgensen, W. L. J. Comput. Chem. 1997, 18, 1955.
12. Jorgensen, W. L., et al. Theochem. 1998, 424, 145.
13. McDonald, N. A., Jorgensen, W. L. J. Phys. Chem. B. 1998, 102, 8049.
14. Rizzo, R. C.; Jorgensen, W. L. J. Am. Chem. Soc. 1999, 121, 4827.
15. Watkins, E. K.; Jorgensen, W. L., J. Phys. Chem. A. 2001, 205, 4118.
16. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2001, 105, 6474.
17. OPLSAA/L reparameterization, version 1 torsions used for SER, version 1 for ASP, version 3 (combined) for LEU, VAL, Jacobson, M.P., et al. J. Phys. Chem. B. 2002, 106, 11673. The charges for HISE used in this force field have not been published to our knowledge.
18. Jensen, K. P.; Jorgensen, W. L. J. Chem. Theory Comput. 2006, 2, 1499.
19. Jacobson, M.P.; Kaminski, G. A.; Friesner, R. A.; Rapp, C. S. J. Phys. Chem. B. 2002, 106, 11673.
20. Berendsen, H. J. C. et al. in Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht,1981), p. 331.
21. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269.
22. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926. Parameters as tabulated in Mahoney, M. W.; Jorgensen, W. L. J. Chem. Phys. 2000, 112, 8910.
23. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902.
24. Jorgensen, W. L.; Madura, J. D. Mol. Phys. 1985, 56, 1381. Parameters as tabulated in Mahoney, M. W.; Jorgensen, W. L. J. Chem. Phys. 2000, 112, 8910.
25. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L. J. Chem. Phys. 2004, 120, 9665.
26. Mahoney, M. W.; Jorgensen, W. L. J. Chem. Phys. 2000, 112, 8910.
27. Earl D. J; Deem, M. W.; Phys. Chem. Chem. Phys., 2005, 7, 3910.
28. Guo Z; Mohanty U.; Noehre J.; Sawyer T. K.; Sherman W.; Krilov G. Probing the α-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis. Chem. Biol. Drug Des. 2010, 75, 348.
29. Patriksson, A; van der Spoel, D., A temperature predictor for parallel tempering simulations. Phys. Chem. Chem. Phys. 2008, 10, 2073.
30. Gervasio, F. L.; Laio, A.; Parrinello, M. Flexible docking in solution using metadynamics. J. Am. Chem. Soc. 2005, 127, 2600.
31. Shivakumar, D.; Williams, J.; Wu, Y.; Damm, W.; Shelley, J.; Sherman, W. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field. J. Chem. Theory Comput. 2010, 6, 1509.
32. Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J., Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13749.
33. Wang, L.; Berne, B. J.; Friesner, R. A. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 1937.
34. Wang, L.; Friesner, R. A.; Berne, B. J. Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2). J. Phys. Chem. B 2011, 115, 9431.
35. Todeschini, R.; Lasagni, M.; Marengo, E. New Molecular Descriptors for 2D and 3D Structures. Theory. J. Chemom. 1994, 8, 263.
36. Amadei, A.; Linssen, A. B.; Berendsen, H. J. Essential dynamics of proteins. Proteins 1993, 17, 412.
37. Predescu, C.; Lerer, A. K.; Lippert, R. A.; Towles, B.; Grossman, J. P.; Dirks, R. M.; Shaw, D. E. The u-series: A separable decomposition for electrostatics computation with improved accuracy. J. Chem. Phys. 2020, 084113. DOI: 10.1063/1.5129393