Boresch S - Search Results

1

Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies.

de Ruiter A, Boresch S, Oostenbrink C. de Ruiter A, et al. Among authors: boresch s. J Comput Chem. 2013 May 5;34(12):1024-34. doi: 10.1002/jcc.23229. Epub 2013 Jan 19. J Comput Chem. 2013. PMID: 23335287

2

Unorthodox uses of Bennett's acceptance ratio method.

König G, Bruckner S, Boresch S. König G, et al. Among authors: boresch s. J Comput Chem. 2009 Aug;30(11):1712-8. doi: 10.1002/jcc.21255. J Comput Chem. 2009. PMID: 19373838

3

Hydration free energies of amino acids: why side chain analog data are not enough.

König G, Boresch S. König G, et al. Among authors: boresch s. J Phys Chem B. 2009 Jul 2;113(26):8967-74. doi: 10.1021/jp902638y. J Phys Chem B. 2009. PMID: 19507836

4

Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.

König G, Boresch S. König G, et al. Among authors: boresch s. J Comput Chem. 2011 Apr 30;32(6):1082-90. doi: 10.1002/jcc.21687. Epub 2010 Nov 4. J Comput Chem. 2011. PMID: 21387335

5

Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method.

Bruckner S, Boresch S. Bruckner S, et al. Among authors: boresch s. J Comput Chem. 2011 May;32(7):1303-19. doi: 10.1002/jcc.21713. Epub 2010 Dec 31. J Comput Chem. 2011. PMID: 21425288

6

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration.

Bruckner S, Boresch S. Bruckner S, et al. Among authors: boresch s. J Comput Chem. 2011 May;32(7):1320-33. doi: 10.1002/jcc.21712. Epub 2010 Dec 31. J Comput Chem. 2011. PMID: 21425289

7

Avoiding the van der Waals endpoint problem using serial atomic insertion.

Boresch S, Bruckner S. Boresch S, et al. J Comput Chem. 2011 Aug;32(11):2449-58. doi: 10.1002/jcc.21829. Epub 2011 May 23. J Comput Chem. 2011. PMID: 21607991

8

Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program.

Wieder M, Fleck M, Braunsfeld B, Boresch S. Wieder M, et al. Among authors: boresch s. J Comput Chem. 2022 Jun 30;43(17):1151-1160. doi: 10.1002/jcc.26877. Epub 2022 Apr 29. J Comput Chem. 2022. PMID: 35485139 Free PMC article.

9

Transport and dielectric properties of water and the influence of coarse-graining: comparing BMW, SPC/E, and TIP3P models.

Braun D, Boresch S, Steinhauser O. Braun D, et al. Among authors: boresch s. J Chem Phys. 2014 Feb 14;140(6):064107. doi: 10.1063/1.4864117. J Chem Phys. 2014. PMID: 24527900

10

Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes.

Hudson PS, White JK, Kearns FL, Hodoscek M, Boresch S, Lee Woodcock H. Hudson PS, et al. Among authors: boresch s. Biochim Biophys Acta. 2015 May;1850(5):944-953. doi: 10.1016/j.bbagen.2014.09.016. Epub 2014 Sep 17. Biochim Biophys Acta. 2015. PMID: 25239198

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