Igor S Tolokh
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Explore the profile of Igor S Tolokh including associated specialties, affiliations and a list of published articles.
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19
Citations
197
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Recent Articles
1.
Forouzesh N, Ghafouri F, Tolokh I, Onufriev A
J Chem Inf Model
. 2024 Dec;
64(24):9433-9448.
PMID: 39656550
Accuracy of binding free energy calculations utilizing implicit solvent models is critically affected by parameters of the underlying dielectric boundary, specifically, the atomic and water probe radii. Here, a multidimensional...
2.
Tolokh I, Folescu D, Onufriev A
J Phys Chem B
. 2024 Jun;
128(24):5855-5873.
PMID: 38860842
The current practical "workhorses" of the atomistic implicit solvation─the Poisson-Boltzmann (PB) and generalized Born (GB) models─face fundamental accuracy limitations. Here, we propose a computationally efficient implicit solvation framework, the Implicit...
3.
Afanasyev A, Kim Y, Tolokh I, Sharakhov I, Onufriev A
Epigenetics Chromatin
. 2024 May;
17(1):13.
PMID: 38705995
Background: Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear,...
4.
Bass L, Elder L, Folescu D, Forouzesh N, Tolokh I, Karpatne A, et al.
J Chem Theory Comput
. 2023 Dec;
20(1):396-410.
PMID: 38149593
The accuracy of computational models of water is key to atomistic simulations of biomolecules. We propose a computationally efficient way to improve the accuracy of the prediction of hydration-free energies...
5.
Tolokh I, Kinney N, Sharakhov I, Onufriev A
Epigenetics Chromatin
. 2023 May;
16(1):21.
PMID: 37254161
Background: Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional (3D) chromatin structure and dynamics;...
6.
Tolokh I, Thomas D, Onufriev A
J Chem Phys
. 2018 Oct;
148(19):195101.
PMID: 30307229
The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model...
7.
Katz A, Tolokh I, Pabit S, Baker N, Onufriev A, Pollack L
Biophys J
. 2017 Jan;
112(1):22-30.
PMID: 28076812
Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells...
8.
Drozdetski A, Tolokh I, Pollack L, Baker N, Onufriev A
Phys Rev Lett
. 2016 Jul;
117(2):028101.
PMID: 27447528
Increasing the concentration of counterions (salt) is known to reduce the bending persistence length of DNA. Here we use atomistic molecular dynamics simulations to predict that multivalent counterions have the...
9.
Tolokh I, Drozdetski A, Pollack L, Baker N, Onufriev A
J Chem Phys
. 2016 Jul;
144(15):155101.
PMID: 27389241
We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution...
10.
Pabit S, Katz A, Tolokh I, Drozdetski A, Baker N, Onufriev A, et al.
J Chem Phys
. 2016 Jun;
144(20):205102.
PMID: 27250330
Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering...