List of works - Alexey Onufriev

A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules

scientific article published in 2022

A strategy for reducing gross errors in the generalized Born models of implicit solvation.

scientific article

Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies

scientific article published on 29 January 2018

Accuracy limit of rigid 3-point water models

scientific article published on August 2016

Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.

scientific article published on May 2014

Accurate evaluation of charge asymmetry in aqueous solvation. ⬇️

scientific article published on 7 May 2015

Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models ⬇️

scientific article published on August 7, 2012

Charge State of the Globular Histone Core Controls Stability of the Nucleosome ⬇️

scientific article published on September 8, 2010

Chromosome-nuclear envelope attachments affect interphase chromosome territories and entanglement.

scientific article

Explicit ions/implicit water generalized Born model for nucleic acids

scientific article published on 01 May 2018

Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator

scientific article published on 14 November 2019

General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins

scientific article published on 26 March 2019

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies

scientific article published on 8 August 2017

Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber

scientific article published on 17 October 2016

MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor

scientific article published on 26 August 2020

Modeling of Flap Endonuclease Interactions with DNA Substrate ⬇️

scientific article published on May 2, 2003

Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core

scientific article published on 16 March 2018

Multi-shell model of ion-induced nucleic acid condensation. ⬇️

scientific article published on April 2016

Point Charges Optimally Placed to Represent the Multipole Expansion of Charge Distributions ⬇️

scientific article published on July 4, 2013

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle ⬇️

scientific article published on October 3, 2003

Protonation and pK changes in protein-ligand binding.

scientific article published on May 2013

Similarities and Differences between Na<sup>+</sup> and K<sup>+</sup> Distributions around DNA Obtained with Three Popular Water Models

scientific article published on 11 October 2021

Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

scientific article published on 11 May 2022

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

scientific article published in January 2019

Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes

scientific article published on 01 February 2020

Why Computed Protein Folding Landscapes Are Sensitive to the Water Model

scientific article published on 20 December 2018

List of works by Alexey Onufriev