Publications by authors named "AV Onufriev"

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Quantifying conformational heterogeneity of 3D genome organization in fruit fly.
Samira Mali, Igor S Tolokh, Erik Cross, Alexey V Onufriev

PLoS One· July 2025

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Using Deep Graph Neural Networks Improves Physics-Based Hydration Free Energy Predictions Even for Molecules Outside of the Training Set Distribution.
Luke H Elder, Alexey V Onufriev

J Phys Chem B· July 2025

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Quantifying Conformational Heterogeneity of 3D Genome Organization in Fruit Fly.
Samira Mali, Igor S Tolokh, Erik Cross, Alexey V Onufriev

bioRxiv· May 2025

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Multiplateau Force-Extension Curves of Long Double-Stranded DNA Molecules.
Alexander Y Afanasyev, Alexey V Onufriev

ACS Omega· April 2025

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Multi-plateau force-extension curves of long double-stranded DNA molecules.
Alexander Y Afanasyev, Alexey V Onufriev

bioRxiv· February 2025

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Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.
Negin Forouzesh, Fatemeh Ghafouri, Igor S Tolokh, Alexey V Onufriev

J Chem Inf Model· December 2024

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Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.
Egor S Kolesnikov, Yeyue Xiong, Alexey V Onufriev

J Chem Theory Comput· October 2024

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Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains.
Igor S Tolokh, Dan E Folescu, Alexey V Onufriev

J Phys Chem B· June 2024

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The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies.
Alexander Y Afanasyev, Yoonjin Kim, Igor S Tolokh, Igor V Sharakhov, Alexey V Onufriev

Epigenetics Chromatin· May 2024

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Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment.
Lewis Bass, Luke H Elder, Dan E Folescu, Negin Forouzesh, Igor S Tolokh, Alexey V Onufriev

J Chem Theory Comput· January 2024

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AmberTools.
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, G Andrés Cisneros, Alexey V Onufriev

J Chem Inf Model· October 2023

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Why Na+ has higher propensity than K+ to condense DNA in a crowded environment.
Egor S Kolesnikov, Ivan Yu Gushchin, Petr A Zhilyaev, Alexey V Onufriev

J Chem Phys· October 2023

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Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.
Igor S Tolokh, Nicholas Allen Kinney, Igor V Sharakhov, Alexey V Onufriev

Epigenetics Chromatin· May 2023

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Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome.
Alexey V Onufriev

Front Mol Biosci· April 2023

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Correction to "Fast Polarizable Water Model for Atomistic Simulations".
Yeyue Xiong, Saeed Izadi, Alexey V Onufriev

J Chem Theory Comput· January 2023

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Fast Polarizable Water Model for Atomistic Simulations.
Yeyue Xiong, Saeed Izadi, Alexey V Onufriev

J Chem Theory Comput· October 2022

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A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules.
Dan E Folescu, Alexey V Onufriev

ACS Omega· August 2022

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Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach.
Alexander Y Afanasyev, Alexey V Onufriev

J Chem Theory Comput· June 2022

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Similarities and Differences between Na and K Distributions around DNA Obtained with Three Popular Water Models.
Egor S Kolesnikov, Ivan Yu Gushchin, Petr A Zhilyaev, Alexey V Onufriev

J Chem Theory Comput· November 2021

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How to Count Bugs: A Method to Estimate the Most Probable Absolute Population Density and Its Statistical Bounds from a Single Trap Catch.
Ksenia S Onufrieva, Alexey V Onufriev

Insects· October 2021

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Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure.
Parviz Seifpanahi Shabane, Alexey V Onufriev

J Mol Biol· March 2021

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Bounds on Absolute Gypsy Moth () (Lepidoptera: Erebidae) Population Density as Derived from Counts in Single Milk Carton Traps.
Ksenia S Onufrieva, Alexey V Onufriev, Andrea D Hickman, James R Miller

Insects· October 2020

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Melting Points of OPC and OPC3 Water Models.
Yeyue Xiong, Parviz Seifpanahi Shabane, Alexey V Onufriev

ACS Omega· October 2020

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MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor.
Negin Forouzesh, Alexey V Onufriev

bioRxiv· August 2020

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Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment.
Aleksander V Drozdetski, Abhishek Mukhopadhyay, Alexey V Onufriev

Front Phys· November 2019

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