Ge Y - Search Results

1

Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.

Ge Y, Melling OJ, Dong W, Essex JW, Mobley DL. Ge Y, et al. J Comput Aided Mol Des. 2022 Oct;36(10):767-779. doi: 10.1007/s10822-022-00479-w. Epub 2022 Oct 6. J Comput Aided Mol Des. 2022. PMID: 36198874 Free PMC article.

2

A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations.

Ge Y, Hahn DF, Mobley DL. Ge Y, et al. J Chem Inf Model. 2021 Mar 22;61(3):1048-1052. doi: 10.1021/acs.jcim.0c01424. Epub 2021 Mar 9. J Chem Inf Model. 2021. PMID: 33686853 Free PMC article.

3

Temperature artifacts in protein structures bias ligand-binding predictions.

Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. Bradford SYC, et al. Among authors: ge y. Chem Sci. 2021 Jul 13;12(34):11275-11293. doi: 10.1039/d1sc02751d. eCollection 2021 Sep 1. Chem Sci. 2021. PMID: 34667539 Free PMC article.

4

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.

Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. Ge Y, et al. J Chem Theory Comput. 2022 Mar 8;18(3):1359-1381. doi: 10.1021/acs.jctc.1c00590. Epub 2022 Feb 11. J Chem Theory Comput. 2022. PMID: 35148093 Free PMC article.

5

Absolute Binding Free Energy Calculations for Buried Water Molecules.

Ge Y, Baumann HM, Mobley DL. Ge Y, et al. J Chem Theory Comput. 2022 Nov 8;18(11):6482-6499. doi: 10.1021/acs.jctc.2c00658. Epub 2022 Oct 5. J Chem Theory Comput. 2022. PMID: 36197451 Free PMC article.

6

An overview of the SAMPL8 host-guest binding challenge.

Amezcua M, Setiadi J, Ge Y, Mobley DL. Amezcua M, et al. Among authors: ge y. J Comput Aided Mol Des. 2022 Oct;36(10):707-734. doi: 10.1007/s10822-022-00462-5. Epub 2022 Oct 14. J Comput Aided Mol Des. 2022. PMID: 36229622 Free PMC article.

7

Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods.

Breznik M, Ge Y, Bluck JP, Briem H, Hahn DF, Christ CD, Mortier J, Mobley DL, Meier K. Breznik M, et al. Among authors: ge y. ChemMedChem. 2023 Jan 3;18(1):e202200425. doi: 10.1002/cmdc.202200425. Epub 2022 Nov 29. ChemMedChem. 2023. PMID: 36240514 Free PMC article.

8

Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo.

Melling OJ, Samways ML, Ge Y, Mobley DL, Essex JW. Melling OJ, et al. Among authors: ge y. J Chem Theory Comput. 2023 Feb 14;19(3):1050-1062. doi: 10.1021/acs.jctc.2c00823. Epub 2023 Jan 24. J Chem Theory Comput. 2023. PMID: 36692215 Free PMC article.

9

Leveraging a Separation of States Method for Relative Binding Free Energy Calculations in Systems with Trapped Waters.

Wagle S, Merz PT, Ge Y, Bayly CI, Mobley DL. Wagle S, et al. Among authors: ge y. J Chem Theory Comput. 2024 Dec 24;20(24):11013-11031. doi: 10.1021/acs.jctc.4c01145. Epub 2024 Dec 9. J Chem Theory Comput. 2024. PMID: 39652747 Free PMC article.

10

Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling.

Ge Y, Voelz VA. Ge Y, et al. J Chem Phys. 2022 Apr 7;156(13):134115. doi: 10.1063/5.0088024. J Chem Phys. 2022. PMID: 35395889 Free PMC article.

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