Radak B - Search Results

1

Exploring the effects of habitat management on grassland biodiversity: A case study from northern Serbia.

Milić D, Rat M, Bokić B, Mudri-Stojnić S, Milošević N, Sukur N, Jakovetić D, Radak B, Tot T, Vujanović D, Anačkov G, Radišić D. Milić D, et al. Among authors: radak b. PLoS One. 2024 Mar 28;19(3):e0301391. doi: 10.1371/journal.pone.0301391. eCollection 2024. PLoS One. 2024. PMID: 38547306 Free PMC article.

2

Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences.

Li P, Li Z, Wang Y, Dou H, Radak BK, Allen BK, Sherman W, Xu H. Li P, et al. Among authors: radak bk. J Chem Theory Comput. 2022 Feb 8;18(2):650-663. doi: 10.1021/acs.jctc.1c00703. Epub 2021 Dec 6. J Chem Theory Comput. 2022. PMID: 34871502

3

Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units.

Ben-Shalom IY, Lin C, Radak BK, Sherman W, Gilson MK. Ben-Shalom IY, et al. Among authors: radak bk. J Chem Theory Comput. 2021 Dec 14;17(12):7366-7372. doi: 10.1021/acs.jctc.1c00867. Epub 2021 Nov 11. J Chem Theory Comput. 2021. PMID: 34762421 Free PMC article.

4

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.

Ben-Shalom IY, Lin Z, Radak BK, Lin C, Sherman W, Gilson MK. Ben-Shalom IY, et al. Among authors: radak bk. J Chem Theory Comput. 2020 Dec 8;16(12):7883-7894. doi: 10.1021/acs.jctc.0c00785. Epub 2020 Nov 18. J Chem Theory Comput. 2020. PMID: 33206520 Free PMC article.

5

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Lee TS, Allen BK, Giese TJ, Guo Z, Li P, Lin C, McGee TD Jr, Pearlman DA, Radak BK, Tao Y, Tsai HC, Xu H, Sherman W, York DM. Lee TS, et al. Among authors: radak bk. J Chem Inf Model. 2020 Nov 23;60(11):5595-5623. doi: 10.1021/acs.jcim.0c00613. Epub 2020 Sep 16. J Chem Inf Model. 2020. PMID: 32936637 Free PMC article.

6

Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD.

Chen H, Maia JDC, Radak BK, Hardy DJ, Cai W, Chipot C, Tajkhorshid E. Chen H, et al. Among authors: radak bk. J Chem Inf Model. 2020 Nov 23;60(11):5301-5307. doi: 10.1021/acs.jcim.0c00745. Epub 2020 Sep 1. J Chem Inf Model. 2020. PMID: 32805108 Free PMC article.

7

Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, Wang Y, Roux B, Aksimentiev A, Luthey-Schulten Z, Kalé LV, Schulten K, Chipot C, Tajkhorshid E. Phillips JC, et al. Among authors: radak bk. J Chem Phys. 2020 Jul 28;153(4):044130. doi: 10.1063/5.0014475. J Chem Phys. 2020. PMID: 32752662 Free PMC article.

8

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.

Lee TS, Lin Z, Allen BK, Lin C, Radak BK, Tao Y, Tsai HC, Sherman W, York DM. Lee TS, et al. Among authors: radak bk. J Chem Theory Comput. 2020 Sep 8;16(9):5512-5525. doi: 10.1021/acs.jctc.0c00237. Epub 2020 Aug 12. J Chem Theory Comput. 2020. PMID: 32672455 Free PMC article.

9

Rigorous Free Energy Simulations in Virtual Screening.

Cournia Z, Allen BK, Beuming T, Pearlman DA, Radak BK, Sherman W. Cournia Z, et al. Among authors: radak bk. J Chem Inf Model. 2020 Sep 28;60(9):4153-4169. doi: 10.1021/acs.jcim.0c00116. Epub 2020 Jun 16. J Chem Inf Model. 2020. PMID: 32539386

10

Finite-sample bias in free energy bridge estimators.

Radak BK. Radak BK. J Chem Phys. 2019 Jul 21;151(3):034105. doi: 10.1063/1.5097384. J Chem Phys. 2019. PMID: 31325916 Free PMC article.

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