Okur A - Search Results

1

MSCALE: A General Utility for Multiscale Modeling.

Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW, Brooks BR. Woodcock HL, et al. Among authors: okur a. J Chem Theory Comput. 2011 Apr 12;7(4):1208-1219. doi: 10.1021/ct100738h. J Chem Theory Comput. 2011. PMID: 21691425 Free PMC article.

2

Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.

Okur A, Miller BT, Joo K, Lee J, Brooks BR. Okur A, et al. J Chem Theory Comput. 2013 Feb 1;9(2):1115-1124. doi: 10.1021/ct300996m. J Chem Theory Comput. 2013. PMID: 23585739 Free PMC article.

3

Reservoir pH replica exchange.

Damjanovic A, Miller BT, Okur A, Brooks BR. Damjanovic A, et al. Among authors: okur a. J Chem Phys. 2018 Aug 21;149(7):072321. doi: 10.1063/1.5027413. J Chem Phys. 2018. PMID: 30134701 Free PMC article.

4

MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.

Smith DB, Okur A, Brooks B. Smith DB, et al. Among authors: okur a. Chem Phys Lett. 2012 Aug 30;545:118-124. doi: 10.1016/j.cplett.2012.07.015. Epub 2012 Jul 19. Chem Phys Lett. 2012. PMID: 23087450 Free PMC article.

5

Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models.

Okur A, Wickstrom L, Simmerling C. Okur A, et al. J Chem Theory Comput. 2008 Mar;4(3):488-98. doi: 10.1021/ct7002308. J Chem Theory Comput. 2008. PMID: 26620789

6

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model.

Okur A, Wickstrom L, Layten M, Geney R, Song K, Hornak V, Simmerling C. Okur A, et al. J Chem Theory Comput. 2006 Mar;2(2):420-33. doi: 10.1021/ct050196z. J Chem Theory Comput. 2006. PMID: 26626529

7

Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir.

Okur A, Roe DR, Cui G, Hornak V, Simmerling C. Okur A, et al. J Chem Theory Comput. 2007 Mar;3(2):557-68. doi: 10.1021/ct600263e. J Chem Theory Comput. 2007. PMID: 26637035

8

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.

Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C. Roe DR, et al. Among authors: okur a. J Phys Chem B. 2007 Feb 22;111(7):1846-57. doi: 10.1021/jp066831u. Epub 2007 Jan 27. J Phys Chem B. 2007. PMID: 17256983 Free PMC article.

9

Improving the description of salt bridge strength and geometry in a Generalized Born model.

Shang Y, Nguyen H, Wickstrom L, Okur A, Simmerling C. Shang Y, et al. Among authors: okur a. J Mol Graph Model. 2011 Feb;29(5):676-84. doi: 10.1016/j.jmgm.2010.11.013. Epub 2010 Dec 2. J Mol Graph Model. 2011. PMID: 21168352 Free PMC article.

10

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: okur a. 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.

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