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Alexey Onufriev
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The Amber biomolecular simulation programs
DA Case, TE Cheatham, T Darden, H Gohlke, R Luo, KM Merz, A Onufriev, ...
Journal of computational chemistry 26 (16), 1668-1688, 2005
97732005
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
54632021
Exploring protein native states and large‐scale conformational changes with a modified generalized born model
A Onufriev, D Bashford, DA Case
Proteins: Structure, Function, and Bioinformatics 55 (2), 383-394, 2004
26362004
H++: a server for estimating p Ka s and adding missing hydrogens to macromolecules
JC Gordon, JB Myers, T Folta, V Shoja, LS Heath, A Onufriev
Nucleic acids research 33 (suppl_2), W368-W371, 2005
16112005
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
R Anandakrishnan, B Aguilar, AV Onufriev
Nucleic Acids Research 40 (W1), W537-W541, 2012
15822012
Modification of the generalized Born model suitable for macromolecules
A Onufriev, D Bashford, A David
The Journal of Physical Chemistry B 104 (15), 3712-3720, 2000
12182000
Building water models: a different approach
S Izadi, R Anandakrishnan, AV Onufriev
The journal of physical chemistry letters 5 (21), 3863-3871, 2014
8372014
Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
M Feig, A Onufriev, MS Lee, W Im, DA Case, CL Brooks
Journal of computational chemistry 25 (2), 265-284, 2003
7282003
Effective Born radii in the generalized Born approximation: the importance of being perfect
A Onufriev, DA Case, D Bashford
Journal of computational chemistry 23 (14), 1297-1304, 2002
5612002
Generalized Born model with a simple, robust molecular volume correction
J Mongan, C Simmerling, JA McCammon, DA Case, A Onufriev
Journal of chemical theory and computation 3 (1), 156-169, 2007
4402007
A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
J Myers, G Grothaus, S Narayanan, A Onufriev
Proteins: Structure, Function, and Bioinformatics 63 (4), 928-938, 2006
3512006
Accuracy limit of rigid 3-point water models
S Izadi, AV Onufriev
The Journal of chemical physics 145 (7), 2016
2642016
AMBER 2018, University of California, San Francisco, 2018
DA Case, JT Berryman, RM Betz, DS Cerutti, TE Cheatham III, TA Darden, ...
There is no corresponding record for this reference, 2015
2502015
A novel view of pH titration in biomolecules
A Onufriev, A David, GM Ullmann
Biochemistry 40 (12), 3413-3419, 2001
2422001
AmberTools
DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ...
Journal of chemical information and modeling 63 (20), 6183-6191, 2023
2172023
Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations
R Anandakrishnan, A Drozdetski, RC Walker, AV Onufriev
Biophysical journal 108 (5), 1153-1164, 2015
2132015
Generalized Born implicit solvent models for biomolecules
AV Onufriev, DA Case
Annual review of biophysics 48 (1), 275-296, 2019
2122019
Water models for biomolecular simulations
AV Onufriev, S Izadi
Wiley Interdisciplinary Reviews: Computational Molecular Science 8 (2), e1347, 2018
1832018
Protonation and pK changes in protein–ligand binding
AV Onufriev, E Alexov
Quarterly reviews of biophysics 46 (2), 181-209, 2013
1832013
Analytical electrostatics for biomolecules: Beyond the generalized Born approximation
G Sigalov, A Fenley, A Onufriev
The Journal of chemical physics 124 (12), 2006
1592006
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Articles 1–20