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Page 1
Exploring cryo-electron microscopy with molecular dynamics.
Biochem Soc Trans. 2022 Feb 28;50(1):569-581. doi: 10.1042/BST20210485.
Biochem Soc Trans. 2022.
PMID: 35212361
Review.
Poor Person's pH Simulation of Membrane Proteins.
Gupta C, Khaniya U, Vant JW, Shekhar M, Mao J, Gunner MR, Singharoy A.
Gupta C, et al. Among authors: vant jw.
Methods Mol Biol. 2021;2315:197-217. doi: 10.1007/978-1-0716-1468-6_12.
Methods Mol Biol. 2021.
PMID: 34302678
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Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism.
Singharoy A, Maffeo C, Delgado-Magnero KH, Swainsbury DJK, Sener M, Kleinekathöfer U, Vant JW, Nguyen J, Hitchcock A, Isralewitz B, Teo I, Chandler DE, Stone JE, Phillips JC, Pogorelov TV, Mallus MI, Chipot C, Luthey-Schulten Z, Tieleman DP, Hunter CN, Tajkhorshid E, Aksimentiev A, Schulten K.
Singharoy A, et al. Among authors: vant jw.
Cell. 2019 Nov 14;179(5):1098-1111.e23. doi: 10.1016/j.cell.2019.10.021.
Cell. 2019.
PMID: 31730852
Free PMC article.
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Data-guided Multi-Map variables for ensemble refinement of molecular movies.
Vant JW, Sarkar D, Streitwieser E, Fiorin G, Skeel R, Vermaas JV, Singharoy A.
Vant JW, et al.
J Chem Phys. 2020 Dec 7;153(21):214102. doi: 10.1063/5.0022433.
J Chem Phys. 2020.
PMID: 33291927
Free PMC article.
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Molecular Dynamics Flexible Fitting: All You Want to Know About Resolution Exchange.
Vant JW, Sarkar D, Gupta C, Shekhar MS, Mittal S, Singharoy A.
Vant JW, et al.
Methods Mol Biol. 2020;2165:301-315. doi: 10.1007/978-1-0716-0708-4_18.
Methods Mol Biol. 2020.
PMID: 32621233
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Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting.
Sarkar D, Lee H, Vant JW, Turilli M, Vermaas JV, Jha S, Singharoy A.
Sarkar D, et al. Among authors: vant jw.
J Chem Inf Model. 2023 Sep 25;63(18):5834-5846. doi: 10.1021/acs.jcim.3c00350. Epub 2023 Sep 4.
J Chem Inf Model. 2023.
PMID: 37661856
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Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials.
Vant JW, Lahey SJ, Jana K, Shekhar M, Sarkar D, Munk BH, Kleinekathöfer U, Mittal S, Rowley C, Singharoy A.
Vant JW, et al.
J Chem Inf Model. 2020 May 26;60(5):2591-2604. doi: 10.1021/acs.jcim.9b01167. Epub 2020 Mar 30.
J Chem Inf Model. 2020.
PMID: 32207947
Free PMC article.
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