Cerutti DS - Search Results

1

Alchemical prediction of hydration free energies for SAMPL.

Mobley DL, Liu S, Cerutti DS, Swope WC, Rice JE. Mobley DL, et al. Among authors: cerutti ds. J Comput Aided Mol Des. 2012 May;26(5):551-62. doi: 10.1007/s10822-011-9528-8. Epub 2011 Dec 24. J Comput Aided Mol Des. 2012. PMID: 22198475 Free PMC article.

2

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.

3

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.

4

On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge.

Bansal N, Zheng Z, Cerutti DS, Merz KM. Bansal N, et al. Among authors: cerutti ds. J Comput Aided Mol Des. 2017 Jan;31(1):47-60. doi: 10.1007/s10822-016-9980-6. Epub 2016 Oct 3. J Comput Aided Mol Des. 2017. PMID: 27699553

5

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

Cerutti DS, Freddolino PL, 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.

6

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. Harder E, et al. Among authors: cerutti ds. J Chem Theory Comput. 2016 Jan 12;12(1):281-96. doi: 10.1021/acs.jctc.5b00864. Epub 2015 Dec 1. J Chem Theory Comput. 2016. PMID: 26584231

7

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.

Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg A, Case DA, Walker RC, York DM. Lee TS, et al. Among authors: cerutti ds. J Chem Inf Model. 2018 Oct 22;58(10):2043-2050. doi: 10.1021/acs.jcim.8b00462. Epub 2018 Sep 25. J Chem Inf Model. 2018. PMID: 30199633 Free PMC article.

8

Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?

Cerutti DS, Baker NA, McCammon JA. Cerutti DS, et al. J Chem Phys. 2007 Oct 21;127(15):155101. doi: 10.1063/1.2771171. J Chem Phys. 2007. PMID: 17949217 Free PMC article.

9

CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications.

Cerutti DS, Jain T, McCammon JA. Cerutti DS, et al. Protein Sci. 2006 Jul;15(7):1579-96. doi: 10.1110/ps.051985106. Protein Sci. 2006. PMID: 16815913 Free PMC article.

10

Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric.

Cerutti DS, Wong CF, McCammon JA. Cerutti DS, et al. Biopolymers. 2003 Oct;70(3):391-402. doi: 10.1002/bip.10498. Biopolymers. 2003. PMID: 14579311

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