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

por Onufriev, Alexey V.
Publicado 2023

Linear relationship between peak and season-long abundances in insects

por Onufrieva, Ksenia S., Onufriev, Alexey V.
Publicado 2018

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

por Xiong, Yeyue, Onufriev, Alexey V.
Publicado 2019

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

por Forouzesh, Negin, Onufriev, Alexey V.
Publicado 2020

How to Count Bugs: A Method to Estimate the Most Probable Absolute Population Density and Its Statistical Bounds from a Single Trap Catch

por Onufrieva, Ksenia S., Onufriev, Alexey V.
Publicado 2021

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

por Folescu, Dan E., Onufriev, Alexey V.
Publicado 2022

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

por Anandakrishnan, Ramu, Aguilar, Boris, Onufriev, Alexey V.
Publicado 2012

Building Water Models: A Different Approach

por Izadi, Saeed, Anandakrishnan, Ramu, Onufriev, Alexey V.
Publicado 2014

Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

por Drozdetski, Aleksander V., Mukhopadhyay, Abhishek, Onufriev, Alexey V.
Publicado 2019

Melting Points of OPC and OPC3 Water Models

por Xiong, Yeyue, Shabane, Parviz Seifpanahi, Onufriev, Alexey V.
Publicado 2020

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

por Anandakrishnan, Ramu, Baker, Charles, Izadi, Saeed, Onufriev, Alexey V.
Publicado 2013

Investigation of the Chromosome Regions with Significant Affinity for the Nuclear Envelope in Fruit Fly – A Model Based Approach

por Kinney, Nicholas Allen, Sharakhov, Igor V., Onufriev, Alexey V.
Publicado 2014

Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement

por Kinney, Nicholas Allen, Sharakhov, Igor V., Onufriev, Alexey V.
Publicado 2018

Introducing Charge Hydration Asymmetry into the Generalized Born Model

por Mukhopadhyay, Abhishek, Aguilar, Boris H., Tolokh, Igor S., Onufriev, Alexey V.
Publicado 2014

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

por Fenley, Andrew T., Anandakrishnan, Ramu, Kidane, Yared H., Onufriev, Alexey V.
Publicado 2018

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

por Tolokh, Igor S., Kinney, Nicholas Allen, Sharakhov, Igor V., Onufriev, Alexey V.
Publicado 2023

Bounds on Absolute Gypsy Moth (Lymantria dispar dispar) (Lepidoptera: Erebidae) Population Density as Derived from Counts in Single Milk Carton Traps

por Onufrieva, Ksenia S., Onufriev, Alexey V., Hickman, Andrea D., Miller, James R.
Publicado 2020

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

por George, Phillip, Kinney, Nicholas A., Liang, Jiangtao, Onufriev, Alexey V., Sharakhov, Igor V.
Publicado 2020

Why double-stranded RNA resists condensation

por Tolokh, Igor S., Pabit, Suzette A., Katz, Andrea M., Chen, Yujie, Drozdetski, Aleksander, Baker, Nathan, Pollack, Lois, Onufriev, Alexey V.
Publicado 2014

AmberTools

por Case, David A., Aktulga, Hasan Metin, Belfon, Kellon, Cerutti, David S., Cisneros, G. Andrés, Cruzeiro, Vinícius Wilian D., Forouzesh, Negin, Giese, Timothy J., Götz, 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, Thomas E., Roe, Daniel R., Roitberg, Adrian, Simmerling, Carlos, York, Darrin M., Nagan, Maria C., Merz, Kenneth M.
Publicado 2023