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Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory.
Roy D, Kovalenko A. Roy D, et al. Among authors: kovalenko a. Int J Mol Sci. 2021 May 11;22(10):5061. doi: 10.3390/ijms22105061. Int J Mol Sci. 2021. PMID: 34064655 Free PMC article. Review.
The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular …
The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecul …
Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent.
Roy D, Kovalenko A. Roy D, et al. Among authors: kovalenko a. J Comput Aided Mol Des. 2019 Oct;33(10):905-912. doi: 10.1007/s10822-019-00238-4. Epub 2019 Oct 21. J Comput Aided Mol Des. 2019. PMID: 31637566
The molecular solvation theory in the form of the Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko-Hirata (KH) closure relation is benchmarked for use with dimethyl sulfoxide (DMSO) as solvent for (bio)-chemical simulation within the framework of …
The molecular solvation theory in the form of the Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko-Hirata …
The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations.
Hinge VK, Blinov N, Roy D, Wishart DS, Kovalenko A. Hinge VK, et al. Among authors: kovalenko a. J Comput Aided Mol Des. 2019 Oct;33(10):913-926. doi: 10.1007/s10822-019-00239-3. Epub 2019 Nov 4. J Comput Aided Mol Des. 2019. PMID: 31686367
A recent X-ray crystal structure has revealed that 5-Fluorouridine (5-FUrd) binds at the W32 binding site and can act as a pharmacophore scaffold for the development of anti-ALS drugs. ...The docked configuration is within 0.58 A (RMSD) of the observed config …
A recent X-ray crystal structure has revealed that 5-Fluorouridine (5-FUrd) binds at the W32 binding site and can act as a pha …
Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet?
Roy D, Dutta D, Wishart DS, Kovalenko A. Roy D, et al. Among authors: kovalenko a. J Comput Aided Mol Des. 2021 Feb;35(2):261-269. doi: 10.1007/s10822-020-00364-4. Epub 2021 Jan 4. J Comput Aided Mol Des. 2021. PMID: 33392947
PAMPA experiments provide a working mimic of a molecule passing through cells and PAMPA values are widely used to estimate drug absorption parameters. ...We used the three-dimensional reference interaction site model (3D-RISM) theory with the Kovalenko-Hirata …
PAMPA experiments provide a working mimic of a molecule passing through cells and PAMPA values are widely used to estimate dru …
Predicting Accurate Solvation Free Energy in n-Octanol Using 3D-RISM-KH Molecular Theory of Solvation: Making Right Choices.
Roy D, Blinov N, Kovalenko A. Roy D, et al. Among authors: kovalenko a. J Phys Chem B. 2017 Oct 5;121(39):9268-9273. doi: 10.1021/acs.jpcb.7b06375. Epub 2017 Sep 25. J Phys Chem B. 2017. PMID: 28880087
Molecular theory of solvation, a.k.a., three-dimensional reference interaction site model theory of solvation with Kovalenko-Hirata closure relation (3D-RISM-KH), is an accurate and fast theory predicting solvation free energy and structure. ...The best agree …
Molecular theory of solvation, a.k.a., three-dimensional reference interaction site model theory of solvation with Kovalenk …
Performance of 3D-RISM-KH in Predicting Hydration Free Energy: Effect of Solute Parameters.
Roy D, Kovalenko A. Roy D, et al. Among authors: kovalenko a. J Phys Chem A. 2019 May 9;123(18):4087-4093. doi: 10.1021/acs.jpca.9b01623. Epub 2019 Apr 29. J Phys Chem A. 2019. PMID: 30993994
The three-dimensional reference interaction site model molecular solvation theory with the Kovalenko-Hirata closure relation has been shown to produce excellent solvation characteristics for a large class of (bio)chemical systems in solution. ...In order to find out …
The three-dimensional reference interaction site model molecular solvation theory with the Kovalenko-Hirata closure relation has been …
730 results