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Molecular Simulation Volume 37, 2011 - Issue 8: Nanotech 09-10. Guest Editor Fiona Case
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Original Articles

3D-RISM-KH approach for biomolecular modelling at nanoscale: thermodynamics of fibril formation and beyond

Nikolay Blinov Department of Mechanical Engineering, University of Alberta, National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta, Canada, T6G 2M9Correspondence[email protected]
,
Lyudmyla Dorosh Department of Mechanical Engineering, University of Alberta, National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta, Canada, T6G 2M9
,
David Wishart Departments of Biological Sciences and Computing Science, University of Alberta, National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta, Canada, T6G 2M9
&
Andriy Kovalenko Department of Mechanical Engineering, University of Alberta, National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta, Canada, T6G 2M9
Pages 718-728 | Received 24 Sep 2010, Accepted 28 Nov 2010, Published online: 25 Mar 2011

Citations (16)

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Igor Omelyan & Andriy Kovalenko. (2013) Generalised canonical–isokinetic ensemble: speeding up multiscale molecular dynamics and coupling with 3D molecular theory of solvation. Molecular Simulation 39:1, pages 25-48.
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Articles from other publishers (15)

Dipankar Roy & Andriy Kovalenko. (2023) Multiscale Methods Framework with the 3D-RISM-KH Molecular Solvation Theory for Supramolecular Structures, Nanomaterials, and Biomolecules: Where Are We Going?. Thermo 3:3, pages 375-395.
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Rodrigo Aguayo-Ortiz & Laura Dominguez. (2019) Effects of Mutating Trp42 Residue on γD-Crystallin Stability. Journal of Chemical Information and Modeling 60:2, pages 777-785.
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Kamonwan Pacaphol, Kanogwan Seraypheap & Duangdao Aht-Ong. (2019) Development and application of nanofibrillated cellulose coating for shelf life extension of fresh-cut vegetable during postharvest storage. Carbohydrate Polymers 224, pages 115167.
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Rodrigo Aguayo-Ortiz, Augusto González-Navejas, Giovanni Palomino-Vizcaino, Oscar Rodriguez-Meza, Miguel Costas, Liliana Quintanar & Laura Dominguez. (2019) Thermodynamic Stability of Human γD-Crystallin Mutants Using Alchemical Free-Energy Calculations. The Journal of Physical Chemistry B 123:27, pages 5671-5677.
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Andriy Kovalenko & Sergey Gusarov. (2018) Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics. Physical Chemistry Chemical Physics 20:5, pages 2947-2969.
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Andriy Kovalenko. 2017. Springer Handbook of Electrochemical Energy. Springer Handbook of Electrochemical Energy 95 139 .
Alexander E Kobryn, Sergey Gusarov & Andriy Kovalenko. (2016) A closure relation to molecular theory of solvation for macromolecules. Journal of Physics: Condensed Matter 28:40, pages 404003.
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WenJuan Huang, Nikolay Blinov & Andriy Kovalenko. (2015) Octanol–Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction. The Journal of Physical Chemistry B 119:17, pages 5588-5597.
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WenJuan Huang, Nikolay Blinov, David S. Wishart & Andriy Kovalenko. (2015) Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation. Journal of Chemical Information and Modeling 55:2, pages 317-328.
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Andriy Kovalenko. (2014) Predictive Multiscale Modeling of Nanocellulose Based Materials and Systems. IOP Conference Series: Materials Science and Engineering 64, pages 012040.
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Igor Omelyan & Andriy Kovalenko. (2013) Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces. The Journal of Chemical Physics 139:24.
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Andriy Kovalenko. (2013) Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials. Pure and Applied Chemistry 85:1, pages 159-199.
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Sergey Gusarov, Bhalchandra S. Pujari & Andriy Kovalenko. (2012) Efficient treatment of solvation shells in 3D molecular theory of solvation. Journal of Computational Chemistry 33:17, pages 1478-1494.
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Andriy Kovalenko, Alexander E. Kobryn, Sergey Gusarov, Olga Lyubimova, Xiangjun Liu, Nikolay Blinov & Masaru Yoshida. (2012) Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators. Soft Matter 8:5, pages 1508-1520.
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Andriy Kovalenko & Nikolay Blinov. (2011) Multiscale methods for nanochemistry and biophysics in solution. Journal of Molecular Liquids 164:1-2, pages 101-112.
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