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Asim Okur
Asim Okur
Postdoctoral Research Fellow, National Institutes of Health
Verified email at nhlbi.nih.gov
Title
Cited by
Cited by
Year
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
66992006
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
4202006
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
2502009
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
1742006
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
1542007
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
1322006
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
1272003
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
1142007
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
922007
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
632006
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
512008
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
482011
Hybrid explicit/implicit solvation methods
A Okur, C Simmerling
Annual reports in computational chemistry 2, 97-109, 2006
422006
Reservoir pH replica exchange
A Damjanovic, BT Miller, A Okur, BR Brooks
The Journal of Chemical Physics 149 (7), 072321, 2018
232018
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
212011
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
192013
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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Articles 1–20