Asim Okur, Ph.D. - Publications

Affiliations: 
2007 Stony Brook University, Stony Brook, NY, United States 

16 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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