Alexey V. Onufriev

Biochemistry, Genetics and Molecular BiologyPhysics and Astronomy

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 17 papers. Top paper: “AmberTools”.

AmberTools

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c01153

N/A

8.3DataRank · unranked

1950 citations

Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro +42 more

The Amber biomolecular simulation programs

Journal of Computational Chemistry(2005)10.1002/jcc.20290

N/A

1.4DataRank · unranked

9524 citations

Thomas E. Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz +6 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.25.267625

N/A

0DataRank · unranked

13 citations

Alexey V. Onufriev, Negin Forouzesh

Robustness of Multidimensional Optimization Outcomes: A General Approach and a Case Study

PubMed(2020)10.22360/springsim.2020.hpc.004

N/A

0DataRank · unranked

2 citations

Layne T. Watson, Alexey V. Onufriev, Negin Forouzesh

Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails

Nature Communications(2021)10.1038/s41467-021-25568-6

N/A

0DataRank · unranked

109 citations

Shuxiang Li, Alexey V. Onufriev, David Landsman, Anna R. Panchenko, Yunhui Peng

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

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00332

N/A

0DataRank · unranked

29 citations

Ivan Gushchin, Petr Zhilyaev, Alexey V. Onufriev, Egor S. Kolesnikov

Fast Polarizable Water Model for Atomistic Simulations

Journal of Chemical Theory and Computation(2022)10.1021/acs.jctc.2c00378

N/A

0DataRank · unranked

33 citations

Saeed Izadi, Alexey V. Onufriev, Yeyue Xiong

Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.28.478236

N/A

0DataRank · unranked

4 citations

Nicholas A. Kinney, Igor V. Sharakhov, Alexey V. Onufriev, Igor S. Tolokh

A fast polarizable water model for atomistic simulations.

ChemRxiv(2022)10.26434/chemrxiv-2022-v80r5

N/A

0DataRank · unranked

0 citations

Saeed Izadi, Alexey V. Onufriev, Yeyue Xiong

Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

Epigenetics & Chromatin(2023)10.1186/s13072-023-00492-9

N/A

0DataRank · unranked

23 citations

Nicholas A. Kinney, Igor V. Sharakhov, Alexey V. Onufriev, Igor S. Tolokh

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(2023)10.3389/fmolb.2023.1067787

N/A

0DataRank · unranked

8 citations

Alexey V. Onufriev

Multi-plateau force-extension curves of long double-stranded DNA molecules

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.12.532320

N/A

0DataRank · unranked

0 citations

Alexey V. Onufriev, Alexander Y. Afanasyev

Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00833

N/A

0DataRank · unranked

9 citations

Yeyue Xiong, Alexey V. Onufriev, Egor S. Kolesnikov

Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent

ChemRxiv(2024)10.26434/chemrxiv-2024-8hc3r

N/A

0DataRank · unranked

0 citations

Fatemeh Ghafouri, Igor S. Tolokh, Alexey V. Onufriev, Negin Forouzesh

Using Deep Graph Neural Networks Improves Physics-Based Hydration Free Energy Predictions Even for Molecules Outside of the Training Set Distribution

The Journal of Physical Chemistry B(2025)10.1021/acs.jpcb.5c02263

N/A

0DataRank · unranked

2 citations

Alexey V. Onufriev, Luke H. Elder

Using Deep Graph Neural Networks Improves Physics-Based Hydration Free Energy Predictions Even for Molecules Outside of the Training Set Distribution

ChemRxiv(2025)10.26434/chemrxiv-2025-b4b11

N/A

0DataRank · unranked

0 citations

Alexey V. Onufriev, Luke H. Elder

Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure

Journal of Molecular Biology(2020)10.1016/j.jmb.2020.10.017

N/A

0DataRank · unranked

17 citations

Alexey V. Onufriev, Parviz Seifpanahi Shabane