Alexey Onufriev
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
AMBER 2015
DA Case, J Berryman, RM Betz, DS Cerutti, TE Cheatham Iii, TA Darden, ...
University of California, 2015
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
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
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
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
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
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
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
Building water models: a different approach
S Izadi, R Anandakrishnan, AV Onufriev
The journal of physical chemistry letters 5 (21), 3863-3871, 2014
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
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
A novel view of pH titration in biomolecules
A Onufriev, A David, GM Ullmann
Biochemistry 40 (12), 3413-3419, 2001
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
Amber 2015 (University of California, San Francisco)
DA Case, DS Cerutti, TE Cheatham, TA Darden, RE Duke, TJ Giese, ...
Available from ambermd. org/doc12/Amber15. pdf, 2015
Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
JZ Ruscio, D Kumar, M Shukla, MG Prisant, TM Murali, AV Onufriev
Proceedings of the National Academy of Sciences 105 (27), 9204-9209, 2008
Protonation and pK changes in protein–ligand binding
AV Onufriev, E Alexov
Quarterly reviews of biophysics 46 (2), 181-209, 2013
Accuracy limit of rigid 3-point water models
S Izadi, AV Onufriev
The Journal of chemical physics 145 (7), 074501, 2016
Analytical electrostatics for biomolecules: Beyond the generalized Born approximation
G Sigalov, A Fenley, A Onufriev
The Journal of chemical physics 124 (12), 124902, 2006
Implicit solvent models in molecular dynamics simulations: A brief overview
A Onufriev
Annual Reports in Computational Chemistry 4, 125-137, 2008
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