Ries B - Search Results

1

Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties.

Comeau C, Ries B, Stadelmann T, Tremblay J, Poulet S, Fröhlich U, Côté J, Boudreault PL, Derbali RM, Sarret P, Grandbois M, Leclair G, Riniker S, Marsault É. Comeau C, et al. Among authors: ries b. J Med Chem. 2021 May 13;64(9):5365-5383. doi: 10.1021/acs.jmedchem.0c02036. Epub 2021 Mar 22. J Med Chem. 2021. PMID: 33750117

2

Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations.

Ries B, Linker SM, Hahn DF, König G, Riniker S. Ries B, et al. J Chem Inf Model. 2021 Feb 22;61(2):560-564. doi: 10.1021/acs.jcim.0c01283. Epub 2021 Jan 29. J Chem Inf Model. 2021. PMID: 33512157

3

Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy.

Weiß RG, Ries B, Wang S, Riniker S. Weiß RG, et al. Among authors: ries b. J Chem Phys. 2021 Feb 28;154(8):084106. doi: 10.1063/5.0025797. J Chem Phys. 2021. PMID: 33639726

4

Passing the Barrier - How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides.

Linker SM, Wang S, Ries B, Stadelmann T, Riniker S. Linker SM, et al. Among authors: ries b. Chimia (Aarau). 2021 Jun 30;75(6):518-521. doi: 10.2533/chimia.2021.518. Chimia (Aarau). 2021. PMID: 34233816 Free article.

5

Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling.

König G, Ries B, Hünenberger PH, Riniker S. König G, et al. Among authors: ries b. J Chem Theory Comput. 2021 Sep 14;17(9):5805-5815. doi: 10.1021/acs.jctc.1c00418. Epub 2021 Sep 3. J Chem Theory Comput. 2021. PMID: 34476947

6

Recent developments in multiscale free energy simulations.

Barros EP, Ries B, Böselt L, Champion C, Riniker S. Barros EP, et al. Among authors: ries b. Curr Opin Struct Biol. 2022 Feb;72:55-62. doi: 10.1016/j.sbi.2021.08.003. Epub 2021 Sep 14. Curr Opin Struct Biol. 2022. PMID: 34534706 Free article. Review.

7

Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure.

Ries B, Normak K, Weiß RG, Rieder S, Barros EP, Champion C, König G, Riniker S. Ries B, et al. J Comput Aided Mol Des. 2022 Feb;36(2):117-130. doi: 10.1007/s10822-021-00436-z. Epub 2022 Jan 3. J Comput Aided Mol Des. 2022. PMID: 34978000 Free PMC article.

8

RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology.

Ries B, Rieder S, Rhiner C, Hünenberger PH, Riniker S. Ries B, et al. J Comput Aided Mol Des. 2022 Mar;36(3):175-192. doi: 10.1007/s10822-022-00445-6. Epub 2022 Mar 22. J Comput Aided Mol Des. 2022. PMID: 35314898 Free PMC article.

9

Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability.

Linker SM, Schellhaas C, Ries B, Roth HJ, Fouché M, Rodde S, Riniker S. Linker SM, et al. Among authors: ries b. RSC Adv. 2022 Feb 16;12(10):5782-5796. doi: 10.1039/d1ra09025a. eCollection 2022 Feb 16. RSC Adv. 2022. PMID: 35424539 Free PMC article.

10

Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules.

Rieder SR, Ries B, Schaller K, Champion C, Barros EP, Hünenberger PH, Riniker S. Rieder SR, et al. Among authors: ries b. J Chem Inf Model. 2022 Jun 27;62(12):3043-3056. doi: 10.1021/acs.jcim.2c00383. Epub 2022 Jun 8. J Chem Inf Model. 2022. PMID: 35675713 Free PMC article.

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