Zhang BW - Search Results

1

Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.

Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Xia J, et al. Among authors: zhang bw. J Comput Chem. 2015 Sep 5;36(23):1772-85. doi: 10.1002/jcc.23996. Epub 2015 Jul 7. J Comput Chem. 2015. PMID: 26149645 Free PMC article.

2

Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.

Tan Z, Xia J, Zhang BW, Levy RM. Tan Z, et al. Among authors: zhang bw. J Chem Phys. 2016 Jan 21;144(3):034107. doi: 10.1063/1.4939768. J Chem Phys. 2016. PMID: 26801020 Free PMC article.

3

Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

Zhang BW, Dai W, Gallicchio E, He P, Xia J, Tan Z, Levy RM. Zhang BW, et al. J Phys Chem B. 2016 Aug 25;120(33):8289-301. doi: 10.1021/acs.jpcb.6b02015. Epub 2016 Apr 29. J Phys Chem B. 2016. PMID: 27079355 Free PMC article.

4

The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations.

Zhang BW, Cui D, Matubayasi N, Levy RM. Zhang BW, et al. J Phys Chem B. 2018 May 3;122(17):4700-4707. doi: 10.1021/acs.jpcb.8b02666. Epub 2018 Apr 23. J Phys Chem B. 2018. PMID: 29634902 Free PMC article.

5

Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses.

Sakae Y, Zhang BW, Levy RM, Deng N. Sakae Y, et al. Among authors: zhang bw. J Comput Chem. 2020 Jan 5;41(1):56-68. doi: 10.1002/jcc.26078. Epub 2019 Oct 17. J Comput Chem. 2020. PMID: 31621932 Free PMC article.

6

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

Deng N, Zhang BW, Levy RM. Deng N, et al. Among authors: zhang bw. J Chem Theory Comput. 2015 Jun 9;11(6):2868-78. doi: 10.1021/acs.jctc.5b00264. J Chem Theory Comput. 2015. PMID: 26236174 Free PMC article.

7

A Stochastic Solution to the Unbinned WHAM Equations.

Zhang BW, Xia J, Tan Z, Levy RM. Zhang BW, et al. J Phys Chem Lett. 2015 Oct 1;6(19):3834-40. doi: 10.1021/acs.jpclett.5b01771. Epub 2015 Sep 14. J Phys Chem Lett. 2015. PMID: 26722879 Free PMC article.

8

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

Levy RM, Cui D, Zhang BW, Matubayasi N. Levy RM, et al. Among authors: zhang bw. J Phys Chem B. 2017 Apr 20;121(15):3825-3841. doi: 10.1021/acs.jpcb.6b12889. Epub 2017 Feb 28. J Phys Chem B. 2017. PMID: 28186751 Free PMC article. Review.

9

Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium.

Zhang BW, Deng N, Tan Z, Levy RM. Zhang BW, et al. J Chem Theory Comput. 2017 Oct 10;13(10):4660-4674. doi: 10.1021/acs.jctc.7b00651. Epub 2017 Sep 28. J Chem Theory Comput. 2017. PMID: 28902500 Free PMC article.

10

Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.

He P, Zhang BW, Arasteh S, Wang L, Abel R, Levy RM. He P, et al. Among authors: zhang bw. J Phys Chem Lett. 2018 Aug 2;9(15):4428-4435. doi: 10.1021/acs.jpclett.8b01851. Epub 2018 Jul 24. J Phys Chem Lett. 2018. PMID: 30024165 Free PMC article.

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