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Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation.
Blinov N, Wishart DS, Kovalenko A. Blinov N, et al. Among authors: kovalenko a. J Phys Chem B. 2019 Mar 21;123(11):2491-2506. doi: 10.1021/acs.jpcb.9b00480. Epub 2019 Mar 12. J Phys Chem B. 2019. PMID: 30811210
Structural characterization of amyloid (A)beta peptides implicated in Alzheimer's disease is a challenging problem due to their intrinsically disordered nature and their high propensity for aggregation. ...In this study, we employ the statistical-mechanical, three-d …
Structural characterization of amyloid (A)beta peptides implicated in Alzheimer's disease is a challenging problem due to thei …
Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation.
Stumpe MC, Blinov N, Wishart D, Kovalenko A, Pande VS. Stumpe MC, et al. Among authors: kovalenko a. J Phys Chem B. 2011 Jan 20;115(2):319-28. doi: 10.1021/jp102587q. Epub 2010 Dec 21. J Phys Chem B. 2011. PMID: 21174421 Free PMC article.
However, due to sampling requirements, it is not clear that MD simulations are, indeed, the method of choice to obtain converged densities at a given level of precision. We here compare the calculation of local water densities with two different methods: MD simulations and …
However, due to sampling requirements, it is not clear that MD simulations are, indeed, the method of choice to obtain converged densities a …
Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction.
Huang W, Blinov N, Kovalenko A. Huang W, et al. Among authors: kovalenko a. J Phys Chem B. 2015 Apr 30;119(17):5588-97. doi: 10.1021/acs.jpcb.5b01291. Epub 2015 Apr 15. J Phys Chem B. 2015. PMID: 25844645
The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. ...Here …
The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new …
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 …
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 …
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