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Journal of Biomolecular Structure and Dynamics Volume 34, 2016 - Issue 1
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Articles

Importance of long-time simulations for rare event sampling in zinc finger proteins

Ryan GodwinDepartment of Physics, Wake Forest University, Winston-Salem, NC27109, USAView further author information
,
William GmeinerDepartment of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, NC27107, USAView further author information
&
Freddie R. Salsbury Jr.Department of Physics, Wake Forest University, Winston-Salem, NC27109, USACorrespondence[email protected]
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Pages 125-134 | Received 04 Nov 2014, Accepted 01 Feb 2015, Published online: 09 Apr 2015

Citations (12)

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Read on this site (2)

Jiajie Xiao, Ryan L. Melvin & Freddie R. Salsbury$suffix/text()$suffix/text(). (2019) Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning. Journal of Biomolecular Structure and Dynamics 37:4, pages 982-999.
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Jiajie Xiao & Freddie R. Salsbury. (2017) Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin. Journal of Biomolecular Structure and Dynamics 35:15, pages 3354-3369.
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Articles from other publishers (10)

Dizhou Wu & Freddie R. SalsburyJrJr. (2022) Simulations suggest double sodium binding induces unexpected conformational changes in thrombin. Journal of Molecular Modeling 28:5.
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Philip Horx & Armin Geyer. (2021) High five! Methyl probes at five ring positions of phenylalanine explore the hydrophobic core dynamics of zinc finger miniproteins. Chemical Science 12:34, pages 11455-11463.
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Dizhou Wu, Jiajie Xiao & Freddie R. SalsburyJr.Jr.. (2021) Light Chain Mutation Effects on the Dynamics of Thrombin. Journal of Chemical Information and Modeling 61:2, pages 950-965.
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Ly H. Nguyen, Tuyen T. Tran, Lien Thi Ngoc Truong, Hanh Hong Mai & Toan T. Nguyen. (2020) Overcharging of the Zinc Ion in the Structure of the Zinc-Finger Protein Is Needed for DNA Binding Stability. Biochemistry 59:13, pages 1378-1390.
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Roy González-Alemán, David Hernández-Castillo, Julio Caballero & Luis A. Montero-Cabrera. (2019) Quality Threshold Clustering of Molecular Dynamics: A Word of Caution. Journal of Chemical Information and Modeling 60:2, pages 467-472.
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Ryan L. Melvin, Jiajie Xiao, Kenneth S. Berenhaut, Ryan C. Godwin & Freddie R. Salsbury. (2018) Using correlated motions to determine sufficient sampling times for molecular dynamics. Physical Review E 98:2.
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Ryan L. Melvin, Jiajie Xiao, Ryan C. Godwin, Kenneth S. Berenhaut & Freddie R. SalsburyJr.Jr.. (2018) Visualizing correlated motion with HDBSCAN clustering. Protein Science 27:1, pages 62-75.
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Ryan C. Godwin, Ryan L. Melvin, William H. Gmeiner & Freddie R. SalsburyJr.Jr.. (2017) Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator). Biochemistry 56:4, pages 623-633.
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Ryan L. Melvin, Ryan C. Godwin, Jiajie Xiao, William G. Thompson, Kenneth S. Berenhaut & Freddie R. SalsburyJr.Jr.. (2016) Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge. Journal of Chemical Theory and Computation 12:12, pages 6130-6146.
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Ryan C. Godwin, Ryan Melvin & Freddie R. SalsburyJr.Jr.. 2016. Computer-Aided Drug Discovery. Computer-Aided Drug Discovery 1 30 .

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