Cerutti DS - Search Results

1

Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models.

Cerutti DS, Freddolino L, Duke RE Jr, Case DA. Cerutti DS, et al. J Phys Chem B. 2010 Oct 14;114(40):12811-24. doi: 10.1021/jp105813j. J Phys Chem B. 2010. PMID: 20860388 Free PMC article.

2

Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics.

Cerutti DS, Duke R, Freddolino L, Fan H, Lybrand TP. Cerutti DS, et al. J Chem Theory Comput. 2008 Oct 14;4(10):1669-1680. doi: 10.1021/ct8002173. J Chem Theory Comput. 2008. PMID: 19180249 Free PMC article.

3

Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.

Cerutti DS, Le Trong I, Stenkamp RE, Lybrand TP. Cerutti DS, et al. J Phys Chem B. 2009 May 14;113(19):6971-85. doi: 10.1021/jp9010372. J Phys Chem B. 2009. PMID: 19374419 Free PMC article.

4

Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.

Cerutti DS, Duke RE, Darden TA, Lybrand TP. Cerutti DS, et al. J Chem Theory Comput. 2009 Sep 8;5(9):2322. doi: 10.1021/ct9001015. J Chem Theory Comput. 2009. PMID: 20174456 Free PMC article.

5

Multi-Level Ewald: A hybrid multigrid / Fast Fourier Transform approach to the electrostatic particle-mesh problem.

Cerutti DS, Case DA. Cerutti DS, et al. J Chem Theory Comput. 2010;6(2):443-58. doi: 10.1021/ct900522g. J Chem Theory Comput. 2010. PMID: 22039358 Free PMC article.

6

Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.

Cerutti DS, Rice JE, Swope WC, Case DA. Cerutti DS, et al. J Phys Chem B. 2013 Feb 28;117(8):2328-38. doi: 10.1021/jp311851r. Epub 2013 Feb 18. J Phys Chem B. 2013. PMID: 23379664 Free PMC article.

7

Peptide crystal simulations reveal hidden dynamics.

Janowski PA, Cerutti DS, Holton J, Case DA. Janowski PA, et al. Among authors: cerutti ds. J Am Chem Soc. 2013 May 29;135(21):7938-48. doi: 10.1021/ja401382y. Epub 2013 May 16. J Am Chem Soc. 2013. PMID: 23631449 Free PMC article.

8

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.

Cerutti DS, Swope WC, Rice JE, Case DA. Cerutti DS, et al. J Chem Theory Comput. 2014 Oct 14;10(10):4515-4534. doi: 10.1021/ct500643c. Epub 2014 Sep 18. J Chem Theory Comput. 2014. PMID: 25328495 Free PMC article.

9

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.

Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT. Debiec KT, et al. Among authors: cerutti ds. J Chem Theory Comput. 2016 Aug 9;12(8):3926-47. doi: 10.1021/acs.jctc.6b00567. Epub 2016 Jul 22. J Chem Theory Comput. 2016. PMID: 27399642 Free PMC article.

10

Molecular Dynamics of Oxazole Yellow Dye in its Ground and First Excited Electronic States in Solution and when Intercalated in dsDNA.

Jin C, Cerutti D, Cukier RI. Jin C, et al. J Phys Chem B. 2017 Nov 9;121(44):10242-10248. doi: 10.1021/acs.jpcb.7b08187. Epub 2017 Oct 25. J Phys Chem B. 2017. PMID: 29022340

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