Alexey V Onufriev (Alexey Onufriev)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 31

Top Venues

Journal of chemical theory and computation

The journal of physical chemistry. B

Epigenetics & chromatin

The Journal of chemical physics

Virginia Tech

Brown University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Virginia Tech

United States

professor

Education History

Brown University

United States

PHD :: Physics

Publications

Egor S Kolesnikov, Yeyue Xiong, Alexey V Onufriev
Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA. Journal of chemical theory and computation (2024)
Igor S Tolokh, Dan E Folescu, Alexey V Onufriev
Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains. The journal of physical chemistry. B (2024)
Igor S Tolokh, Dan E Folescu, Alexey V Onufriev
Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains. The journal of physical chemistry. B 128 (24) (2024)
Igor S Tolokh, Dan E Folescu, Alexey V Onufriev
Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains. The journal of physical chemistry. B 128 (24) (2024)
Igor S Tolokh, Dan E Folescu, Alexey V Onufriev
Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains. The journal of physical chemistry. B 128 (24) (2024)
Egor S Kolesnikov, Ivan Yu Gushchin, Petr A Zhilyaev, Alexey V Onufriev
Why Na+ has higher propensity than K+ to condense DNA in a crowded environment. The Journal of chemical physics 159 (14) (2023)
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, Gerardo Andrés Cisneros, Vinícius Wilian D Cruzeiro, Negin Forouzesh, Timothy J Giese, Andreas W Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet C Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R Machado, Hai Minh Nguyen, Kurt A O'Hearn, Alexey V Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E Cheatham, Daniel R Roe, Adrian E Roitberg, Carlos L Simmerling, Darrin M York, Maria C Nagan, Kenneth M Merz
AmberTools. Journal of chemical information and modeling (2023)
Lewis Bass, Luke H Elder, Dan E Folescu, Negin Forouzesh, Igor S Tolokh, Anuj Karpatne, Alexey V Onufriev
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 20 (1) (2023)
Lewis Bass, Luke H Elder, Dan E Folescu, Negin Forouzesh, Igor S Tolokh, Anuj Karpatne, Alexey V Onufriev
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 (2023)
Lewis Bass, Luke H Elder, Dan E Folescu, Negin Forouzesh, Igor S Tolokh, Anuj Karpatne, Alexey V Onufriev
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 20 (1) (2023)
Lewis Bass, Luke H Elder, Dan E Folescu, Negin Forouzesh, Igor S Tolokh, Anuj Karpatne, Alexey V Onufriev
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 20 (1) (2023)
Lewis Bass, Luke H Elder, Dan E Folescu, Negin Forouzesh, Igor S Tolokh, Anuj Karpatne, Alexey V Onufriev
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 20 (1) (2023)
Yeyue Xiong, Saeed Izadi, Alexey V Onufriev
Fast Polarizable Water Model for Atomistic Simulations. Journal of chemical theory and computation 18 (10) (2022)
Yeyue Xiong, Saeed Izadi, Alexey V Onufriev
Correction to "Fast Polarizable Water Model for Atomistic Simulations". Journal of chemical theory and computation 19 (1) (2022)
Dan E Folescu, Alexey V Onufriev
A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules. ACS omega 7 (30) (2022)
Alexander Y Afanasyev, Alexey V Onufriev
Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach. Journal of chemical theory and computation 18 (6) (2022)
Yeyue Xiong, Saeed Izadi, Alexey V Onufriev
Correction to "Fast Polarizable Water Model for Atomistic Simulations". Journal of chemical theory and computation (2022)
Egor S Kolesnikov, Ivan Yu Gushchin, Petr A Zhilyaev, Alexey V Onufriev
Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models. Journal of chemical theory and computation 17 (11) (2021)
Yunhui Peng, Shuxiang Li, Alexey V Onufriev, David Landsman, Anna R Panchenko
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails. Nature communications 12 (1) (2021)
Phillip George, Nicholas A Kinney, Jiangtao Liang, Alexey V Onufriev, Igor V Sharakhov
Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes. Cells 9 (2) (2020)
Negin Forouzesh, Abhishek Mukhopadhyay, Layne T Watson, Alexey V Onufriev
Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding. Journal of chemical theory and computation 16 (7) (2020)
Negin Forouzesh, Alexey V Onufriev
MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor. bioRxiv : the preprint server for biology (2020)
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey V Onufriev, David van der Spoel, Anders Wallqvist
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS computational biology 15 (1) (2019)
Yeyue Xiong, Alexey V Onufriev
Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator. PloS one 14 (11) (2019)
Parviz Seifpanahi Shabane, Saeed Izadi, Alexey V Onufriev
General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins. Journal of chemical theory and computation 15 (4) (2019)
Ramu Anandakrishnan, Saeed Izadi, Alexey V Onufriev
Why Computed Protein Folding Landscapes Are Sensitive to the Water Model. Journal of chemical theory and computation 15 (1) (2018)
Igor S Tolokh, Dennis G Thomas, Alexey V Onufriev
Explicit ions/implicit water generalized Born model for nucleic acids. The Journal of chemical physics 148 (19) (2018)
Nicholas Allen Kinney, Igor V Sharakhov, Alexey V Onufriev
Chromosome-nuclear envelope attachments affect interphase chromosome territories and entanglement. Epigenetics & chromatin 11 (1) (2018)
Andrew T Fenley, Ramu Anandakrishnan, Yared H Kidane, Alexey V Onufriev
Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core. Epigenetics & chromatin 11 (1) (2018)
Saeed Izadi, Robert C Harris, Marcia O Fenley, Alexey V Onufriev
Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies. Journal of chemical theory and computation 14 (3) (2018)
Negin Forouzesh, Saeed Izadi, Alexey V Onufriev
Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies. Journal of chemical information and modeling 57 (10) (2017)

Alexey V Onufriev.css-eqlu8i{font-size:small;padding-left:4px;} (Alexey Onufriev)

Publication Activity (10 Years)

Top Topics

Top Venues

Alexey V Onufriev (Alexey Onufriev)