| Year |
Citation |
Score |
| 2018 |
Damjanovic A, Miller BT, Okur A, Brooks BR. Reservoir pH replica exchange. The Journal of Chemical Physics. 149: 072321. PMID 30134701 DOI: 10.1063/1.5027413 |
0.405 |
|
| 2015 |
Damjanovic A, Miller BT, Okur A, Garcia-Moreno B, Brooks BR. Constant pH Simulations with the Double Reservoir pH Replica Exchange Biophysical Journal. 108: 47a. DOI: 10.1016/J.Bpj.2014.11.290 |
0.355 |
|
| 2013 |
Okur A, Miller BT, Joo K, Lee J, Brooks BR. Generating reservoir conformations for replica exchange through the use of the conformational space annealing method. Journal of Chemical Theory and Computation. 9: 1115-1124. PMID 23585739 DOI: 10.1021/Ct300996M |
0.481 |
|
| 2012 |
Smith DB, Okur A, Brooks B. MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods. Chemical Physics Letters. 545: 118-124. PMID 23087450 DOI: 10.1016/J.Cplett.2012.07.015 |
0.489 |
|
| 2012 |
Smith DB, Okur A, Brooks BR. MDMS: Molecular dynamics meta-simulator for evaluating exchange type sampling methods Chemical Physics Letters. 545: 118-124. DOI: 10.1016/j.cplett.2012.07.015 |
0.313 |
|
| 2011 |
Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW, Brooks BR. MSCALE: A General Utility for Multiscale Modeling. Journal of Chemical Theory and Computation. 7: 1208-1219. PMID 21691425 DOI: 10.1021/Ct100738H |
0.441 |
|
| 2011 |
Shang Y, Nguyen H, Wickstrom L, Okur A, Simmerling C. Improving the description of salt bridge strength and geometry in a Generalized Born model. Journal of Molecular Graphics & Modelling. 29: 676-84. PMID 21168352 DOI: 10.1016/J.Jmgm.2010.11.013 |
0.798 |
|
| 2009 |
Wickstrom L, Okur A, Simmerling C. Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophysical Journal. 97: 853-6. PMID 19651043 DOI: 10.1016/J.Bpj.2009.04.063 |
0.791 |
|
| 2008 |
Okur A, Wickstrom L, Simmerling C. Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models. Journal of Chemical Theory and Computation. 4: 488-98. PMID 26620789 DOI: 10.1021/Ct7002308 |
0.802 |
|
| 2007 |
Okur A, Roe DR, Cui G, Hornak V, Simmerling C. Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir. Journal of Chemical Theory and Computation. 3: 557-68. PMID 26637035 DOI: 10.1021/ct600263e |
0.789 |
|
| 2007 |
Roitberg AE, Okur A, Simmerling C. Coupling of replica exchange simulations to a non-Boltzmann structure reservoir. The Journal of Physical Chemistry. B. 111: 2415-8. PMID 17300191 DOI: 10.1021/Jp068335B |
0.676 |
|
| 2007 |
Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. The Journal of Physical Chemistry. B. 111: 1846-57. PMID 17256983 DOI: 10.1021/Jp066831U |
0.767 |
|
| 2006 |
Okur A, Wickstrom L, Layten M, Geney R, Song K, Hornak V, Simmerling C. Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model. Journal of Chemical Theory and Computation. 2: 420-33. PMID 26626529 DOI: 10.1021/Ct050196Z |
0.803 |
|
| 2006 |
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 65: 712-25. PMID 16981200 DOI: 10.1002/Prot.21123 |
0.746 |
|
| 2006 |
Wickstrom L, Okur A, Song K, Hornak V, Raleigh DP, Simmerling CL. The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure. Journal of Molecular Biology. 360: 1094-107. PMID 16797585 DOI: 10.1016/J.Jmb.2006.04.070 |
0.785 |
|
| 2006 |
Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. Journal of the American Chemical Society. 128: 2812-3. PMID 16506755 DOI: 10.1021/Ja058211X |
0.651 |
|
| 2006 |
Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 103: 915-20. PMID 16418268 DOI: 10.1073/Pnas.0508452103 |
0.668 |
|
| 2006 |
Okur A, Simmerling C. Chapter 6 Hybrid Explicit/Implicit Solvation Methods Annual Reports in Computational Chemistry. 2: 97-109. DOI: 10.1016/S1574-1400(06)02006-8 |
0.698 |
|
| 2003 |
Okur A, Strockbine B, Hornak V, Simmerling C. Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. Journal of Computational Chemistry. 24: 21-31. PMID 12483672 DOI: 10.1002/Jcc.10184 |
0.751 |
|
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