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Journal of Biomolecular Structure and Dynamics Volume 37, 2019 - Issue 4
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Research Article

Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning

Jiajie XiaoDepartment of Physics, Wake Forest University, Winston-Salem, NC, USA;Department of Computer Science, Wake Forest University, Winston-Salem, NC, USA
,
Ryan L. MelvinDepartment of Physics, Wake Forest University, Winston-Salem, NC, USA;Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, NC, USA
&
Freddie R. Salsbury JrDepartment of Physics, Wake Forest University, Winston-Salem, NC, USACorrespondence[email protected]
Pages 982-999 | Received 13 Dec 2017, Accepted 17 Feb 2018, Published online: 02 Mar 2018

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Balaji Wamanrao Matore, Partha Pratim Roy & Jagadish Singh. (2023) Discovery of novel VEGFR2-TK inhibitors by phthalimide pharmacophore based virtual screening, molecular docking, MD simulation and DFT. Journal of Biomolecular Structure and Dynamics 41:22, pages 13056-13077.
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Zhipeng Tang, Yujie Ren & Fei Liu. (2022) Identify thrombin inhibitor with novel skeleton based on virtual screening study. Journal of Biomolecular Structure and Dynamics 40:1, pages 499-507.
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Qiankun Wang, Shan Zhang, Zhongjie Han, Huifang Fan & Chunhua Li. (2021) An investigation into the allosteric mechanism of GPCR A2A adenosine receptor with trajectory-based information theory and complex network model. Journal of Biomolecular Structure and Dynamics 39:17, pages 6431-6439.
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Ivan Yu. Torshin, Vladimir A. Namiot, Natalia G. Esipova & Vladimir G. Tumanyan. (2021) Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations. Journal of Biomolecular Structure and Dynamics 39:11, pages 4066-4076.
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Romualdo Troisi, Nicole Balasco, Luigi Vitagliano & Filomena Sica. (2021) Molecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites. Journal of Biomolecular Structure and Dynamics 39:6, pages 2199-2209.
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Anjali Patel, Sanjay Tiwari & Prafulla K. Jha. (2020) Molecular interaction between bi-antennary phenylboronic acid and sialic acid using density functional theory and multi-time scale trajectories. Journal of Biomolecular Structure and Dynamics 38:4, pages 1242-1247.
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Articles from other publishers (8)

Dizhou Wu & Freddie R. SalsburyJr.Jr.. (2023) Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods. Journal of Chemical Information and Modeling 63:12, pages 3705-3718.
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Sian Xiao, Gennady M. Verkhivker & Peng Tao. (2023) Machine learning and protein allostery. Trends in Biochemical Sciences 48:4, pages 375-390.
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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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Romualdo Troisi, Nicole Balasco, Ida Autiero, Luigi Vitagliano & Filomena Sica. (2021) Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. International Journal of Molecular Sciences 22:19, pages 10803.
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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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Fangyuan Chen & Guangrong Huang. (2020) Mechanism and inhibition kinetics of peptide P13 as thrombin inhibitor. International Journal of Biological Macromolecules 150, pages 1046-1052.
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Fangyuan Chen, Han Jiang, Wenwei Chen & Guangrong Huang. (2019) Interaction of the synthetic antithrombotic peptide P10 with thrombin: a spectroscopy study. RSC Advances 9:32, pages 18498-18505.
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Jiajie Xiao & Freddie R. Salsbury. (2019) Na + -binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling . Physical Chemistry Chemical Physics 21:8, pages 4320-4330.
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