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Robert I. Cukier - Publications

Affiliations: 
1972- Chemistry Michigan State University, East Lansing, MI 
Area:
Theory and Computation of Protein Structure Function Relations
Website:
https://www.chemistry.msu.edu/faculty-research/emeritus-faculty/robert-i-cukier/
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75 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
2020 Lou H, Cukier RI. A maximum entropy principle approach to a joint probability model for sequences with known neighbor and next neighbor pair probabilities Chemical Physics. 538: 110872. DOI: 10.1016/J.Chemphys.2020.110872  0.505
2018 Lou H, Cukier RI. Reweighting ensemble probabilities with experimental histogram data constraints using a maximum entropy principle. The Journal of Chemical Physics. 149: 234106. PMID 30579321 DOI: 10.1063/1.5050926  0.529
2018 Cukier RI. Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran-Space Pair Residue Probabilities Using a Markov Chain. The Journal of Physical Chemistry. B. PMID 30204435 DOI: 10.1021/Acs.Jpcb.8B05797  0.324
2018 Cukier RI. Generating intrinsically disordered protein conformational ensembles from a Markov chain. The Journal of Chemical Physics. 148: 105102. PMID 29544285 DOI: 10.1063/1.5010428  0.309
2017 Jin C, Cerutti DS, Cukier RI. Molecular Dynamics of Oxazole Yellow Dye in Its Ground and First Excited Electronic State in Solution and When Intercalated in dsDNA. The Journal of Physical Chemistry. B. PMID 29022340 DOI: 10.1021/Acs.Jpcb.7B08187  0.306
2015 Cukier RI. Dihedral angle entropy measures for intrinsically disordered proteins. The Journal of Physical Chemistry. B. 119: 3621-34. PMID 25679039 DOI: 10.1021/Jp5102412  0.314
2014 Cukier RI. Simulations of potentials of mean force for separating a leucine zipper dimer and the basic region of a basic region leucine zipper dimer. The Journal of Physical Chemistry. B. 118: 10341-54. PMID 25124233 DOI: 10.1021/Jp504723M  0.335
2014 Banerjee R, Yan H, Cukier RI. Conformational transition of response regulator RR468 in a two-component system signal transduction process. The Journal of Physical Chemistry. B. 118: 4727-42. PMID 24731214 DOI: 10.1021/Jp4122968  0.329
2014 Banerjee R, Cukier RI. Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory. The Journal of Physical Chemistry. B. 118: 2883-95. PMID 24571787 DOI: 10.1021/Jp412130D  0.318
2013 Liu J, Cukier RI, Bu Y. Bending Vibration-Governed Solvation Dynamics of an Excess Electron in Liquid Acetonitrile Revealed by Ab Initio Molecular Dynamics Simulation. Journal of Chemical Theory and Computation. 9: 4727-34. PMID 26583391 DOI: 10.1021/Ct4002174  0.316
2013 Cukier RI. Variance of a potential of mean force obtained using the weighted histogram analysis method. The Journal of Physical Chemistry. B. 117: 14785-96. PMID 24175967 DOI: 10.1021/Jp407956C  0.309
2012 Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, Kashlev M, Burton ZF. Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. Bmc Biophysics. 5: 11. PMID 22676913 DOI: 10.1186/2046-1682-5-11  0.329
2011 Cukier RI. Ferreting out correlations from trajectory data. The Journal of Chemical Physics. 135: 225103. PMID 22168728 DOI: 10.1063/1.3666007  0.336
2011 Cukier RI. A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper. The Journal of Chemical Physics. 134: 045104. PMID 21280805 DOI: 10.1063/1.3548074  0.328
2010 Cukier RI. How many atoms are required to characterize accurately trajectory fluctuations of a protein? The Journal of Chemical Physics. 132: 245101. PMID 20590215 DOI: 10.1063/1.3435207  0.316
2010 Seibold SA, Singh BN, Zhang C, Kireeva M, Domecq C, Bouchard A, Nazione AM, Feig M, Cukier RI, Coulombe B, Kashlev M, Hampsey M, Burton ZF. Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. Biochimica Et Biophysica Acta. 1799: 575-87. PMID 20478425 DOI: 10.1016/J.Bbagrm.2010.05.002  0.307
2009 Su L, Cukier RI. Hamiltonian replica exchange method study of Escherichia coli and Yersinia pestis HPPK. The Journal of Physical Chemistry. B. 113: 16197-208. PMID 19924845 DOI: 10.1021/Jp903861A  0.448
2009 Su L, Cukier RI. Hamiltonian replica exchange method studies of a leucine zipper dimer. The Journal of Physical Chemistry. B. 113: 9595-605. PMID 19586073 DOI: 10.1021/Jp900309Q  0.444
2009 Wang Z, Zhang L, Chen X, Cukier RI, Bu Y. Excess electron solvation in an imidazolium-based room-temperature ionic liquid revealed by ab initio molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 8222-6. PMID 19469567 DOI: 10.1021/Jp902575S  0.307
2009 Han L, Li H, Cukier RI, Bu Y. Hetero-ring-expansion design for adenine-based DNA motifs: evidence from DFT calculations and molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 4407-12. PMID 19245224 DOI: 10.1021/Jp8088726  0.314
2009 Su L, Cukier RI. An enhanced molecular dynamics study of HPPK-ATP conformation space exploration and ATP binding to HPPK. The Journal of Physical Chemistry. A. 113: 2025-35. PMID 19191740 DOI: 10.1021/Jp808664K  0.463
2009 Cukier RI. Apo adenylate kinase encodes its holo form: a principal component and varimax analysis. The Journal of Physical Chemistry. B. 113: 1662-72. PMID 19159290 DOI: 10.1021/Jp8053795  0.319
2008 Zhang L, Yan S, Cukier RI, Bu Y. Solvation of excess electrons in LiF ionic pair matrix: evidence for a solvated dielectron from ab initio molecular dynamics simulations and calculations. The Journal of Physical Chemistry. B. 112: 3767-72. PMID 18314971 DOI: 10.1021/Jp800381A  0.343
2007 Su L, Cukier RI. Hamiltonian and distance replica exchange method studies of Met-enkephalin. The Journal of Physical Chemistry. B. 111: 12310-21. PMID 17918879 DOI: 10.1021/Jp073314I  0.457
2007 Seibold SA, Cukier RI. A molecular dynamics study comparing a wild-type with a multiple drug resistant HIV protease: differences in flap and aspartate 25 cavity dimensions. Proteins. 69: 551-65. PMID 17623840 DOI: 10.1002/Prot.21535  0.306
2007 Zhang J, Cukier RI, Bu Y. Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks. The Journal of Physical Chemistry. B. 111: 8335-41. PMID 17580864 DOI: 10.1021/Jp073592H  0.302
2007 Liu J, Seibold SA, Rieke CJ, Song I, Cukier RI, Smith WL. Prostaglandin endoperoxide H synthases: peroxidase hydroperoxide specificity and cyclooxygenase activation. The Journal of Biological Chemistry. 282: 18233-44. PMID 17462992 DOI: 10.1074/Jbc.M701235200  0.309
2007 Yao L, Cukier RI, Yan H. Catalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics study. The Journal of Physical Chemistry. B. 111: 4200-10. PMID 17394305 DOI: 10.1021/Jp0673056  0.541
2007 Yan S, Zhang L, Cukier RI, Bu Y. Exploration on regulating factors for proton transfer along hydrogen-bonded water chains. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 8: 944-54. PMID 17387667 DOI: 10.1002/Cphc.200600674  0.319
2007 Yao L, Yan H, Cukier RI. A molecular dynamics study of the ligand release path in yeast cytosine deaminase. Biophysical Journal. 92: 2301-10. PMID 17218460 DOI: 10.1529/Biophysj.106.098921  0.52
2006 Yao L, Yan H, Cukier RI. A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase. The Journal of Physical Chemistry. B. 110: 26320-6. PMID 17181291 DOI: 10.1021/Jp064301S  0.519
2006 Lou H, Cukier RI. Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations. The Journal of Physical Chemistry. B. 110: 24121-37. PMID 17125384 DOI: 10.1021/Jp064303C  0.581
2006 Lou H, Cukier RI. Molecular dynamics of apo-adenylate kinase: a principal component analysis. The Journal of Physical Chemistry. B. 110: 12796-808. PMID 16800615 DOI: 10.1021/Jp061976M  0.568
2006 Yao L, Yan H, Cukier RI. Mechanism of dihydroneopterin aldolase: a molecular dynamics study of the apo enzyme and its product complex. The Journal of Physical Chemistry. B. 110: 1443-56. PMID 16471696 DOI: 10.1021/Jp054854N  0.52
2005 Yao L, Sklenak S, Yan H, Cukier RI. A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminase. The Journal of Physical Chemistry. B. 109: 7500-10. PMID 16851861 DOI: 10.1021/Jp044828+  0.551
2005 Cukier RI, Morillo M. A targeted reweighting method for accelerating the exploration of high-dimensional configuration space. The Journal of Chemical Physics. 123: 234908. PMID 16392950 DOI: 10.1063/1.2137704  0.326
2005 Seibold SA, Mills DA, Ferguson-Miller S, Cukier RI. Water chain formation and possible proton pumping routes in Rhodobacter sphaeroides cytochrome c oxidase: a molecular dynamics comparison of the wild type and R481K mutant. Biochemistry. 44: 10475-85. PMID 16060656 DOI: 10.1021/Bi0502902  0.322
2005 Cukier RI. A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase. Biochimica Et Biophysica Acta. 1706: 134-46. PMID 15620374 DOI: 10.1016/J.Bbabio.2004.10.004  0.3
2005 Krishnamurthy H, Lou H, Kimple A, Vieille C, Cukier RI. Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates. Proteins. 58: 88-100. PMID 15521058 DOI: 10.1002/Prot.20301  0.545
2004 Sklenak S, Yao L, Cukier RI, Yan H. Catalytic mechanism of yeast cytosine deaminase: an ONIOM computational study. Journal of the American Chemical Society. 126: 14879-89. PMID 15535715 DOI: 10.1021/Ja046462K  0.505
2004 Cukier RI. Quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase. Biochimica Et Biophysica Acta. 1656: 189-202. PMID 15178480 DOI: 10.1016/J.Bbabio.2004.03.006  0.331
2004 Cukier RI. Theory and simulation of proton-coupled electron transfer, hydrogen-atom transfer, and proton translocation in proteins. Biochimica Et Biophysica Acta. 1655: 37-44. PMID 15100014 DOI: 10.1016/J.Bbabio.2003.06.011  0.34
2004 Seibold SA, Smith WL, Cukier RI. Peroxidase site of prostaglandin endoperoxide H synthase-1: Docking and molecular dynamics studies with a prostaglandin endoperoxide analog Journal of Physical Chemistry B. 108: 9297-9305. DOI: 10.1021/Jp049844L  0.326
2004 Cukier RI. A temperature-dependent Hartree approach for excess proton transport in hydrogen-bonded chains Chemical Physics. 305: 197-211. DOI: 10.1016/J.Chemphys.2004.06.060  0.352
2002 Cukier RI. A theory that connects proton-coupled electron-transfer and hydrogen-atom transfer reactions Journal of Physical Chemistry B. 106: 1746-1757. DOI: 10.1021/Jp012396M  0.346
2000 Westphal KL, Lydakis-Simantiris N, Cukier RI, Babcock GT. Effects of Sr2+-substitution on the reduction rates of Yz* in PSII membranes--evidence for concerted hydrogen-atom transfer in oxygen evolution. Biochemistry. 39: 16220-9. PMID 11123952 DOI: 10.1021/Bi0018077  0.33
2000 Casado-Pascual J, Denk C, Morillo M, Cukier RI. Relaxation in charge-transfer systems with very large tunnel splitting: A semiclassical stochastic approach Journal of Chemical Physics. 113: 11176-11186. DOI: 10.1063/1.1326907  0.353
1999 Cukier RI. The effect of a strong external field on the electronic dephasing of a solute that is strongly coupled to a solvent Journal of Chemical Physics. 111: 5408-5417. DOI: 10.1063/1.479801  0.316
1998 Cukier RI, Nocera DG. Proton-coupled electron transfer. Annual Review of Physical Chemistry. 49: 337-69. PMID 9933908 DOI: 10.1146/Annurev.Physchem.49.1.337  0.327
1996 Cukier RI. Proton-coupled electron transfer reactions: Evaluation of rate constants Journal of Physical Chemistry. 100: 15428-15443. DOI: 10.1021/Jp961025G  0.321
1995 Zhao XG, Cukier RI. Molecular dynamics and quantum chemistry study of a proton-coupled electron transfer reaction Journal of Physical Chemistry. 99: 945-954. DOI: 10.1021/J100003A017  0.324
1994 Cukier RI. Mechanism for proton-coupled electron-transfer reactions Journal of Physical Chemistry. 98: 2377-2381. DOI: 10.1021/J100060A027  0.31
1993 Morillo M, Cukier RI. Control of proton-transfer reactions with external fields The Journal of Chemical Physics. 98: 4548-4556. DOI: 10.1063/1.465016  0.324
1992 Cukier RI, Nocera DG. On the separation of static and dynamic solvent effects for electron transfer reactions The Journal of Chemical Physics. 97: 7371-7376. DOI: 10.1063/1.463508  0.341
1992 Zaleski JM, Chang CK, Leroi GE, Cukier RI, Nocera DG. Role of solvent dynamics in the charge recombination of a donor/acceptor pair Journal of the American Chemical Society. 114: 3564-3565. DOI: 10.1021/Ja00035A066  0.312
1991 Sheu SY, Cukier RI. Equilibrium, dynamic, and trapping properties of an excess electron in dense helium The Journal of Chemical Physics. 94: 8258-8269. DOI: 10.1063/1.460110  0.323
1990 Morillo M, Cukier RI. On the effects of solvent and intermolecular fluctuations in proton transfer reactions The Journal of Chemical Physics. 92: 4833-4838. DOI: 10.1063/1.457700  0.36
1989 Yang DY, Cukier RI. The transition from nonadiabatic to solvent controlled adiabatic electron transfer: Solvent dynamical effects in the inverted regime The Journal of Chemical Physics. 91: 281-292. DOI: 10.1063/1.457514  0.359
1989 Cukier RI, Morillo M. Solvent effects on proton-transfer reactions The Journal of Chemical Physics. 91: 857-863. DOI: 10.1063/1.457137  0.342
1989 Morillo M, Yang DY, Cukier RI. Solvent dynamical effects on nonadiabatic electron transfer reactions at low temperature The Journal of Chemical Physics. 90: 5711-5719. DOI: 10.1063/1.456427  0.348
1987 Yang DY, Cukier RI. Concentration dependent fluorescence quenching with ionic reactants The Journal of Chemical Physics. 86: 2833-2838. DOI: 10.1063/1.452033  0.31
1981 Tokuyama M, Cukier RI. Dynamics of diffusion-controlled reactions among stationary sinks: Scaling expansion approach The Journal of Chemical Physics. 76: 6202-6214. DOI: 10.1063/1.443023  0.328
1981 Schell M, Kapral R, Cukier RI. Recombination kinetics: Langevin dynamics with a space dependent friction coefficient The Journal of Chemical Physics. 75: 5879-5882. DOI: 10.1063/1.442038  0.347
1980 Cukier RI, Kapral R, Mehaffey JR. Effect of static correlations on the pair friction coefficient The Journal of Chemical Physics. 73: 5254-5258. DOI: 10.1063/1.439953  0.303
1980 Cukier RI, Kapral R, Mehaffey JR, Shin KJ. Microscopic theory of condensed phase chemical reactions. I. Pair phase space kinetic equation The Journal of Chemical Physics. 72: 1830-1843. DOI: 10.1063/1.439301  0.326
1978 Cukier RI, Levine HB, Shuler KE. Nonlinear sensitivity analysis of multiparameter model systems Journal of Computational Physics. 26: 1-42. DOI: 10.1021/J100540A010  0.553
1975 Cukier RI, Schaibly JH, Shuler KE. Study of the sensitivity of coupled reaction systems to uncertainties in rate coefficients. III. Analysis of the approximations The Journal of Chemical Physics. 63: 1140-1149. DOI: 10.1063/1.431440  0.599
1973 Cukier RI, Lakatos-Lindenberg K, Shuler KE. Orthogonal polynomial solutions of the Fokker-Planck equation Journal of Statistical Physics. 9: 137-144. DOI: 10.1007/Bf01016844  0.558
1972 Cukier RI, Lakatos-Lindenberg K. Rotational relaxation of molecules in fluids for reorientations of arbitrary angle The Journal of Chemical Physics. 57: 3427-3435. DOI: 10.1063/1.1678776  0.323
1972 Cukier RI, Shuler KE. On the microscopic conditions for linear macroscopic laws The Journal of Chemical Physics. 57: 316-319. DOI: 10.1063/1.1677962  0.583
1972 Cukier RI, Shuler KE, Weeks JD. On the validity of stochastic rate equations in finite systems with finite-strength interactions Journal of Statistical Physics. 5: 99-112. DOI: 10.1007/Bf01008373  0.673
1970 Cukier RI, Fortuin CM, Shuler KE, Petschek AG, Schaibly JH. Study of the sensitivity of coupled reaction systems to uncertainties in rate coefficients. I Theory The Journal of Chemical Physics. 3873-3878. DOI: 10.1063/1.1680571  0.597
1969 Cukier RI, Deutch JM. Microscopic theory of brownian motion: The multiple-time-scale point of view Physical Review. 177: 240-244. DOI: 10.1103/Physrev.177.240  0.477
1969 Cukier RI, Deutch JM. Spin relaxation: The multiple-time-scale point of view The Journal of Chemical Physics. 50: 142-150.  0.443
1967 Cukier RI, Deutch JM. Entropy production in canonically invariant systems The Journal of Chemical Physics. 46: 3686-3687. DOI: 10.1063/1.1841279  0.445
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