Asim Okur
Asim Okur
Postdoctoral Research Fellow, National Institutes of Health
Verifierad e-postadress på nhlbi.nih.gov
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Comparison of multiple Amber force fields and development of improved protein backbone parameters
V Hornak, R Abel, A Okur, B Strockbine, A Roitberg, C Simmerling
Proteins: Structure, Function, and Bioinformatics 65 (3), 712-725, 2006
59292006
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations
V Hornak, A Okur, RC Rizzo, C Simmerling
Proceedings of the National Academy of Sciences 103 (4), 915-920, 2006
3872006
Evaluating the performance of the ff99SB force field based on NMR scalar coupling data
L Wickstrom, A Okur, C Simmerling
Biophysical journal 97 (3), 853-856, 2009
2302009
Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model
A Okur, L Wickstrom, M Layten, R Geney, K Song, V Hornak, ...
Journal of Chemical Theory and Computation 2 (2), 420-433, 2006
1672006
Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation
DR Roe, A Okur, L Wickstrom, V Hornak, C Simmerling
The Journal of Physical Chemistry B 111 (7), 1846-1857, 2007
1452007
HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state
V Hornak, A Okur, RC Rizzo, C Simmerling
Journal of the American Chemical Society 128 (9), 2812-2813, 2006
1302006
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins
A Okur, B Strockbine, V Hornak, C Simmerling
Journal of computational chemistry 24 (1), 21-31, 2003
1162003
Coupling of replica exchange simulations to a non-Boltzmann structure reservoir
AE Roitberg, A Okur, C Simmerling
The Journal of Physical Chemistry B 111 (10), 2415-2418, 2007
1052007
Improving convergence of replica-exchange simulations through coupling to a high-temperature structure reservoir
A Okur, DR Roe, G Cui, V Hornak, C Simmerling
Journal of Chemical Theory and Computation 3 (2), 557-568, 2007
812007
The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure
L Wickstrom, A Okur, K Song, V Hornak, DP Raleigh, CL Simmerling
Journal of molecular biology 360 (5), 1094-1107, 2006
592006
Evaluation of salt bridge structure and energetics in peptides using explicit, implicit, and hybrid solvation models
A Okur, L Wickstrom, C Simmerling
Journal of Chemical Theory and Computation 4 (3), 488-498, 2008
482008
MSCALE: a general utility for multiscale modeling
HL Woodcock, BT Miller, M Hodoscek, A Okur, JD Larkin, JW Ponder, ...
Journal of chemical theory and computation 7 (4), 1208-1219, 2011
442011
Hybrid explicit/implicit solvation methods
A Okur, C Simmerling
Annual reports in computational chemistry 2, 97-109, 2006
422006
Improving the description of salt bridge strength and geometry in a Generalized Born model
Y Shang, H Nguyen, L Wickstrom, A Okur, C Simmerling
Journal of Molecular Graphics and Modelling 29 (5), 676-684, 2011
222011
Generating reservoir conformations for replica exchange through the use of the conformational space annealing method
A Okur, BT Miller, K Joo, J Lee, BR Brooks
Journal of chemical theory and computation 9 (2), 1115-1124, 2013
172013
Reservoir pH replica exchange
A Damjanovic, BT Miller, A Okur, BR Brooks
The Journal of chemical physics 149 (7), 072321, 2018
152018
MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods
DB Smith, A Okur, BR Brooks
Chemical physics letters 545, 118-124, 2012
72012
Flap structure and dynamics in HIV-1 protease simulations
V Hornak, A Okur, RC Rizzo, CL Simmerling
Abstracts of Papers of the American Chemical Society 231, 2006
22006
Folding kinetics of a B-hairpin: A molecular dynamics study.
A Okur, DR Roe, GL Cui, V Hornak, C Simmerling
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 226, U450-U451, 2003
12003
Constant pH Simulations with the Double Reservoir pH Replica Exchange
A Damjanovic, BT Miller, A Okur, B Garcia-Moreno, BR Brooks
Biophysical Journal 108 (2), 47a, 2015
2015
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Artiklar 1–20