Alexey Onufriev
Virginia Polytechnic Institute and State University
H-index: 48
North America-United States
Top articles of Alexey Onufriev
Title | Journal | Author(s) | Publication Date |
|---|---|---|---|
AmberTools | Journal of chemical information and modeling | David A Case Hasan Metin Aktulga Kellon Belfon David S Cerutti G Andrés Cisneros | 2023/10/8 |
Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin | Epigenetics & Chromatin | Igor S Tolokh Nicholas Allen Kinney Igor V Sharakhov Alexey V Onufriev | 2023/5/30 |
Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein–DNA complexes, including the nucleosome | Frontiers in Molecular Biosciences | Alexey V Onufriev | 2023/4/18 |
Location of a topologically associating domain at the nuclear periphery has no systematic causal effect on its genes transcription levels in drosophila nuclei | Biophysical Journal | Igor S Tolokh Alexander Y Afanasyev Yoonjin Kim Igor V Sharakhov Alexey V Onufriev | 2023/2/10 |
Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment | Journal of Chemical Theory and Computation | Lewis Bass Luke H Elder Dan E Folescu Negin Forouzesh Igor S Tolokh | 2023/12/27 |
Multi-plateau force-extension curves of long double-stranded DNA | bioRxiv | Alexander Y Afanasyev Alexey V Onufriev | 2023 |
Why Na+ has higher propensity than K+ to condense DNA in a crowded environment | The Journal of Chemical Physics | Egor S Kolesnikov Ivan Yu Gushchin Petr A Zhilyaev Alexey V Onufriev | 2023/10/14 |
AMBER 22 reference manual | David A Case Robert E Duke Ross C Walker Nikolai R Skrynnikov Thomas E Cheatham III | 2022 | |
A closed-form, analytical approximation for apparent surface charge and electric field of molecules | ACS omega | Dan E Folescu Alexey V Onufriev | 2022/7/19 |
The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level | bioRxiv | Yoonjin Kim Alexander Y Afanasyev Igor S Tolokh Igor V Sharakhov Alexey V Onufriev | 2022 |
Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach | Journal of Chemical Theory and Computation | Alexander Y Afanasyev Alexey V Onufriev | 2022/5/11 |
Proximity of chromatin to the nuclear envelope, does not, by itself, affect gene expression in drosophila | Biophysical Journal | Yoonjin Kim Alexander Y Afanasyev Igor S Tolokh Igor V Sharakhov Alexey V Onufriev | 2022/2/11 |
3D architecture of Drosophila interphase chromatin is stabilized by relatively strong attractive interactions between highly-dynamic lamina-associated domains and nuclear envelope | Biophysical Journal | Igor S Tolokh Nicholas A Kinney Igor V Sharakhov Alexey V Onufriev | 2022/2/11 |
Single-cell Hi-C: how modeling can augment experiment? | Biophysical Journal | Samira Mali Igor S Tolokh Igor V Sharakhov Alexey V Onufriev | 2022/2/11 |
Fast polarizable water model for atomistic simulations | Journal of chemical theory and computation | Yeyue Xiong Saeed Izadi Alexey V Onufriev | 2022/10/3 |
Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure | Journal of molecular biology | Parviz Seifpanahi Shabane Alexey V Onufriev | 2021/3/19 |
How to count your bugs? | bioRxiv | Ksenia S Onufrieva Alexey V Onufriev | 2021/2/10 |
How to count bugs: a method to estimate the most probable absolute population density and its statistical bounds from a single trap catch | Insects | Ksenia S Onufrieva Alexey V Onufriev | 2021/10/13 |
Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models | Journal of chemical theory and computation | Egor S Kolesnikov Ivan Yu Gushchin Petr A Zhilyaev Alexey V Onufriev | 2021/10/11 |
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails | Nature communications | Yunhui Peng Shuxiang Li Alexey Onufriev David Landsman Anna R Panchenko | 2021/9/6 |
