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Yunhui Ge - Publications

Affiliations: 
2014- Chemistry Temple University, Philadelphia, PA, United States 
Area:
Computational Chemistry
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26 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Raddi RM, Ge Y, Voelz VA. BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations. Journal of Chemical Information and Modeling. PMID 37027181 DOI: 10.1021/acs.jcim.2c01296  0.7
2023 Melling OJ, Samways ML, Ge Y, Mobley DL, Essex JW. Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo. Journal of Chemical Theory and Computation. PMID 36692215 DOI: 10.1021/acs.jctc.2c00823  0.585
2022 Breznik M, Ge Y, Bluck JP, Briem H, Hahn DF, Christ CD, Mortier J, Mobley DL, Meier K. Prioritizing small sets of molecules for synthesis through in-silico tools: A comparison of common ranking methods. Chemmedchem. PMID 36240514 DOI: 10.1002/cmdc.202200425  0.547
2022 Amezcua M, Setiadi J, Ge Y, Mobley DL. An overview of the SAMPL8 host-guest binding challenge. Journal of Computer-Aided Molecular Design. PMID 36229622 DOI: 10.1007/s10822-022-00462-5  0.582
2022 Ge Y, Melling OJ, Dong W, Essex JW, Mobley DL. Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo. Journal of Computer-Aided Molecular Design. PMID 36198874 DOI: 10.1007/s10822-022-00479-w  0.558
2022 Ge Y, Baumann HM, Mobley DL. Absolute Binding Free Energy Calculations for Buried Water Molecules. Journal of Chemical Theory and Computation. PMID 36197451 DOI: 10.1021/acs.jctc.2c00658  0.557
2022 Ge Y, Voelz VA. Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling. The Journal of Chemical Physics. 156: 134115. PMID 35395889 DOI: 10.1063/5.0088024  0.636
2022 Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques. Journal of Chemical Theory and Computation. PMID 35148093 DOI: 10.1021/acs.jctc.1c00590  0.573
2021 Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. Temperature artifacts in protein structures bias ligand-binding predictions. Chemical Science. 12: 11275-11293. PMID 34667539 DOI: 10.1039/d1sc02751d  0.57
2021 Hurley MFD, Northrup JD, Ge Y, Schafmeister CE, Voelz VA. Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution. Journal of Chemical Information and Modeling. PMID 34125519 DOI: 10.1021/acs.jcim.1c00447  0.65
2021 Voelz VA, Ge Y, Raddi RM. Reconciling Simulations and Experiments With BICePs: A Review. Frontiers in Molecular Biosciences. 8: 661520. PMID 34046431 DOI: 10.3389/fmolb.2021.661520  0.704
2021 Ge Y, Zhang S, Erdelyi M, Voelz VA. Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2. Journal of Chemical Information and Modeling. PMID 33905247 DOI: 10.1021/acs.jcim.1c00029  0.656
2021 Ge Y, Voelz VA. Markov State Models to Elucidate Ligand Binding Mechanism. Methods in Molecular Biology (Clifton, N.J.). 2266: 239-259. PMID 33759131 DOI: 10.1007/978-1-0716-1209-5_14  0.654
2021 Ge Y, Hahn DF, Mobley DL. A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. Journal of Chemical Information and Modeling. PMID 33686853 DOI: 10.1021/acs.jcim.0c01424  0.569
2020 Wan H, Ge Y, Razavi A, Voelz VA. Reconciling simulated ensembles of apomyoglobin with experimental HDX data using Bayesian inference and multi-ensemble Markov State Models. Journal of Chemical Theory and Computation. PMID 31917926 DOI: 10.1021/Acs.Jctc.9B01240  0.692
2020 Ge Y, Voelz VA. Efficient Estimation of Binding Kinetics using Scaled Non-Bonded Interactions and Harmonic Restraints Biophysical Journal. 118: 140a. DOI: 10.1016/J.Bpj.2019.11.890  0.609
2020 Ge Y, Raddi RM, Voelz VA. BICePs 2.0: New Tools for Bayesian Inference of Conformational Populations from Theory and Experiment Biophysical Journal. 118: 139a-140a. DOI: 10.1016/J.Bpj.2019.11.888  0.618
2019 Acharyya A, Ge Y, Wu H, DeGrado WF, Voelz VA, Gai F. Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study. The Journal of Physical Chemistry. B. PMID 30694671 DOI: 10.1021/Acs.Jpcb.8B12220  0.636
2019 Acharyya A, Ge Y, Wu H, DeGrado W, Voelz V, Gai F. Exposing the Nucleation Site of Alpha Helix Folding: A Joint Experimental and Simulation Study Biophysical Journal. 116: 310a. DOI: 10.1016/J.Bpj.2018.11.1679  0.617
2019 Ge Y, Voelz V. Using Computational Modeling to Understand the Binding Mechanism of Designed Cyclic β-Hairpin to MDM2 Biophysical Journal. 116: 193a. DOI: 10.1016/J.Bpj.2018.11.1068  0.618
2018 Ge Y, Borne E, Stewart S, Hansen MR, Arturo EC, Jaffe EK, Voelz VA. Simulations of the regulatory ACT domain of human phenylalanine hydroxylase unveil its mechanism of phenylalanine binding. The Journal of Biological Chemistry. PMID 30287685 DOI: 10.1074/Jbc.Ra118.004909  0.67
2018 Liang H, Zhou G, Ge Y, D'Ambrosio EA, Eidem TM, Blanchard C, Shehatou C, Chatare VK, Dunman PM, Valentine AM, Voelz VA, Grimes CL, Andrade RB. Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeus. Bioorganic & Medicinal Chemistry. PMID 29805074 DOI: 10.1016/J.Bmc.2018.05.017  0.583
2018 Ge Y, Voelz VA. Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization. The Journal of Physical Chemistry. B. PMID 29518328 DOI: 10.1021/Acs.Jpcb.7B11871  0.667
2018 Wan H, Ge Y, Razavi A, Voelz V. Reconciling Simulated Ensembles of Apomyoglobin with Experimental HDX Data Biophysical Journal. 114: 680a-681a. DOI: 10.1016/J.Bpj.2017.11.3671  0.641
2018 Ge Y, Jaffe EK, Voelz VA. Binding Pathways of Phenylalanine to the Dimeric Regulatory Domain of Human PAH Reveal a LID Gating Mechanism Biophysical Journal. 114: 226a. DOI: 10.1016/J.Bpj.2017.11.1257  0.603
2017 Ge Y, Kier BL, Andersen NH, Voelz VA. Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models. Journal of Chemical Information and Modeling. PMID 28614661 DOI: 10.1021/Acs.Jcim.7B00132  0.673
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