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Alexey V. Onufriev

Department of Computer Science

43H指数
162论文数
2.6W被引数
收录论文 82
发表时间
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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利用深度图神经网络改进基于物理的水合自由能预测，即使对于训练集分布之外的分子也是如此
errThe Journal of Physical Chemistry B
IF0
err2025-07-11
err0
PREAI
errLuke H. Elder; Alexey V. Onufriev
err分享
err收藏
Multiplateau Force-Extension Curves of Long Double-Stranded DNA Molecules长双链DNA分子的多重力-延伸曲线
errACS OMEGA
IF4.3
err2025-04-01
err0
errOAAI
errAfanasyev, Alexander Y.; Onufriev, Alexey V.
err分享
err收藏
Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-12-10
err0
errOAAI
errForouzesh, Negin; Ghafouri, Fatemeh; Tolokh, Igor S.; Onufriev, Alexey V.
err分享
err收藏
Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-09-16
err2
errOAAI
errKolesnikov, Egor S.; Xiong, Yeyue; Onufriev, Alexey V.
err分享
err收藏
The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies
errEPIGENETICS & CHROMATIN
IF3.5
err2024-05-06
err0
errOAAI
errAfanasyev, Alexander Y.; Kim, Yoonjin; Tolokh, Igor S.; Sharakhov, Igor V.; Onufriev, Alexey V.
err分享
err收藏
Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2023-12-27
err2
errOAAI
errBass, Lewis; Elder, Luke H.; Folescu, Dan E.; Forouzesh, Negin; Tolokh, Igor S.; Karpatne, Anuj; Onufriev, Alexey V.
err分享
err收藏
Why Na+ has higher propensity than K+ to condense DNA in a crowded environment
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2023-10-10
err2
errOAAI
errKolesnikov, Egor S.; Gushchin, Ivan Yu.; Zhilyaev, Petr A.; Onufriev, Alexey V.
err分享
err收藏
The AmberTools
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2023-10-08
err474
errOAAI
errCase, David A.; Aktulga, Hasan Metin; Belfon, Kellon; Cerutti, David S.; Cisneros, G. Andres; Cruzeiro, Vinicus Wilian D.; Forouzesh, Negin; Giese, Timothy J.; Gotz, Andreas W.; Gohlke, Holger; Izadi, Saeed; Kasavajhala, Koushik; Kaymak, Mehmet C.; King, Edward; Kurtzman, Tom; Lee, Tai-Sung; Li, Pengfei; Liu, Jian; Luchko, Tyler; Luo, Ray; Manathunga, Madushanka; Machado, Matias R.; Nguyen, Hai Minh; O'Hearn, Kurt A.; Onufriev, Alexey V.; Pan, Feng; Pantano, Sergio; Qi, Ruxi; Rahnamoun, Ali; Risheh, Ali; Schott-Verdugo, Stephan; Shajan, Akhil; Swails, Jason; Wang, Junmei; Wei, Haixin; Wu, Xiongwu; Wu, Yongxian; Zhang, Shi; Zhao, Shiji; Zhu, Qiang; Cheatham, I. I. I. Thomas E.; Roe, Daniel R.; Roitberg, Adrian; Simmerling, Carlos; York, Darrin M.; Nagan, Maria C.; Merz, Jr Kenneth M.
err分享
err收藏
Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin
errEPIGENETICS & CHROMATIN
IF3.5
err2023-05-30
err3
errOAAI
errTolokh, Igor S.; Kinney, Nicholas Allen; Sharakhov, Igor V.; Onufriev, Alexey V.
err分享
err收藏
Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome生物学相关的细胞内pH的微小变化可能对蛋白质-DNA复合物的稳定性产生重大影响，包括核小体
errFRONTIERS IN MOLECULAR BIOSCIENCES
IF4
err2023-04-18
err4
errOAAI
errOnufriev, Alexey V. V.
err分享
err收藏
Fast Polarizable Water Model for Atomistic Simulations (vol 18, pg 6324, 2022)
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2022-12-23
err1
PREAI
errXiong, Yeyue; Izadi, Saeed; Onufriev, Alexey V.
err分享
err收藏
Fast Polarizable Water Model for Atomistic Simulations
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2022-10-03
err15
errOAAI
errXiong, Yeyue; Izadi, Saeed; Onufriev, Alexey, V
err分享
err收藏
A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules
errACS OMEGA
IF4.3
err2022-07-19
err4
errOAAI
errFolescu, Dan E.; Onufriev, Alexey, V
err分享
err收藏
Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2022-05-11
err4
errOAAI
errAfanasyev, Alexander Y.; Onufriev, Alexey, V
err分享
err收藏
Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2021-10-11
err21
errOAAI
errKolesnikov, Egor S.; Gushchin, Ivan Yu; Zhilyaev, Petr A.; Onufriev, Alexey, V
err分享
err收藏
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails
errNATURE COMMUNICATIONS
IF15.7
err2021-09-06
err49
errOAAI
errPeng, Yunhui; Li, Shuxiang; Onufriev, Alexey; Landsman, David; Panchenko, Anna R.
err分享
err收藏
Melting Points of OPC and OPC3 Water Models
errACS OMEGA
IF4.3
err2020-09-22
err22
errOAAI
errXiong, Yeyue; Shabane, Parviz Seifpanahi; Onufriev, Alexey, V
err分享
err收藏
Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2020-05-25
err10
errOAAI
errForouzesh, Negin; Mukhopadhyay, Abhishek; Watson, Layne T.; Onufriev, Alexey, V
err分享
err收藏
Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes
errCELLS
IF5.2
err2020-02-01
err10
errOAAI
errGeorge, Phillip; Kinney, Nicholas A.; Liang, Jiangtao; Onufriev, Alexey V.; Sharakhov, Igor V.
err分享
err收藏
The nucleosome: from structure to function through physics
errCURRENT OPINION IN STRUCTURAL BIOLOGY
IF7
err2019-06-01
err50
errOAAI
errOnufriev, Alexey, V; Schiessel, Helmut
err分享
err收藏

研究方向

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合作学者
合作期刊
J
J. Andrew McCammon
H 指数: 134 · 论文数: 1.1K
D
David A. Case
H 指数: 107 · 论文数: 518
C
Charles L. Brooks
H 指数: 104 · 论文数: 675
K
Kenneth M. Merz
H 指数: 83 · 论文数: 691
王君玫 封面图
王君玫 (Junmei Wang)
H 指数: 76 · 论文数: 751
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