Simmerling C - Search Results

1

Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket.

Fallon L, Belfon KAA, Raguette L, Wang Y, Stepanenko D, Cuomo A, Guerra J, Budhan S, Varghese S, Corbo CP, Rizzo RC, Simmerling C. Fallon L, et al. Among authors: simmerling c. J Am Chem Soc. 2021 Aug 4;143(30):11349-11360. doi: 10.1021/jacs.1c00556. Epub 2021 Jul 16. J Am Chem Soc. 2021. PMID: 34270232 Free PMC article.

2

k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations.

Chen L, Roe DR, Kochert M, Simmerling C, Miranda-Quintana RA. Chen L, et al. Among authors: simmerling c. bioRxiv [Preprint]. 2024 Mar 8:2024.03.07.583975. doi: 10.1101/2024.03.07.583975. bioRxiv. 2024. Update in: J Chem Theory Comput. 2024 Jul 9;20(13):5583-5597. doi: 10.1021/acs.jctc.4c00308 PMID: 38496504 Free PMC article. Updated. Preprint.

3

All-atom structure prediction and folding simulations of a stable protein.

Simmerling C, Strockbine B, Roitberg AE. Simmerling C, et al. J Am Chem Soc. 2002 Sep 25;124(38):11258-9. doi: 10.1021/ja0273851. J Am Chem Soc. 2002. PMID: 12236726

4

Conformational heterogeneity observed in simulations of a pyrene-substituted DNA.

Cui G, Simmerling C. Cui G, et al. Among authors: simmerling c. J Am Chem Soc. 2002 Oct 16;124(41):12154-64. doi: 10.1021/ja026825l. J Am Chem Soc. 2002. PMID: 12371855

5

Dynamic behavior of DNA base pairs containing 8-oxoguanine.

Cheng X, Kelso C, Hornak V, de los Santos C, Grollman AP, Simmerling C. Cheng X, et al. Among authors: simmerling c. J Am Chem Soc. 2005 Oct 12;127(40):13906-18. doi: 10.1021/ja052542s. J Am Chem Soc. 2005. PMID: 16201812 Free PMC article.

6

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations.

Hornak V, Okur A, Rizzo RC, Simmerling C. Hornak V, et al. Among authors: simmerling c. Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):915-20. doi: 10.1073/pnas.0508452103. Epub 2006 Jan 17. Proc Natl Acad Sci U S A. 2006. PMID: 16418268 Free PMC article.

7

HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state.

Hornak V, Okur A, Rizzo RC, Simmerling C. Hornak V, et al. Among authors: simmerling c. J Am Chem Soc. 2006 Mar 8;128(9):2812-3. doi: 10.1021/ja058211x. J Am Chem Soc. 2006. PMID: 16506755 Free PMC article.

8

The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts.

Layten M, Hornak V, Simmerling C. Layten M, et al. Among authors: simmerling c. J Am Chem Soc. 2006 Oct 18;128(41):13360-1. doi: 10.1021/ja065133k. J Am Chem Soc. 2006. PMID: 17031940 Free PMC article.

9

Molecular simulations reveal a common binding mode for glycosylase binding of oxidatively damaged DNA lesions.

Song K, Kelso C, de los Santos C, Grollman AP, Simmerling C. Song K, et al. Among authors: simmerling c. J Am Chem Soc. 2007 Nov 28;129(47):14536-7. doi: 10.1021/ja075128w. Epub 2007 Nov 8. J Am Chem Soc. 2007. PMID: 17988127 Free PMC article.

10

Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments.

Ding F, Layten M, Simmerling C. Ding F, et al. Among authors: simmerling c. J Am Chem Soc. 2008 Jun 11;130(23):7184-5. doi: 10.1021/ja800893d. Epub 2008 May 15. J Am Chem Soc. 2008. PMID: 18479129 Free PMC article.

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