| Year |
Citation |
Score |
| 2022 |
Olson WK, Li Y, Fenley MO. Insights into DNA Solvation Found in Protein-DNA Structures. Biophysical Journal. PMID 36380591 DOI: 10.1016/j.bpj.2022.11.019 |
0.373 |
|
| 2018 |
Izadi S, Harris RC, Fenley MO, Onufriev AV. Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies. Journal of Chemical Theory and Computation. PMID 29378399 DOI: 10.1021/Acs.Jctc.7B00886 |
0.479 |
|
| 2017 |
Fenley MO, Boschitsch AH, Harris RC. Numerical Diculties Computing Electrostatic Potentials Near Interfaces with the Poisson-Boltzmann Equation. Journal of Chemical Theory and Computation. PMID 28640608 DOI: 10.1021/Acs.Jctc.7B00487 |
0.445 |
|
| 2015 |
Harris RC, Mackoy T, Fenley MO. Problems of Robustness in Poisson-Boltzmann Binding Free Energies. Journal of Chemical Theory and Computation. 11: 705-712. PMID 26528091 DOI: 10.1021/Ct5005017 |
0.441 |
|
| 2015 |
Fenley MO, Harris RC, Mackoy T, Boschitsch AH. Features of CPB: a Poisson-Boltzmann solver that uses an adaptive cartesian grid. Journal of Computational Chemistry. 36: 235-43. PMID 25430617 DOI: 10.1002/Jcc.23791 |
0.487 |
|
| 2014 |
Ovanesyan Z, Medasani B, Fenley MO, Guerrero-García GI, de la Cruz MO, Marucho M. Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments. The Journal of Chemical Physics. 141: 225103. PMID 25494770 DOI: 10.1063/1.4902407 |
0.468 |
|
| 2014 |
Harris RC, Boschitsch AH, Fenley MO. Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation. The Journal of Chemical Physics. 140: 075102. PMID 24559370 DOI: 10.1063/1.4864460 |
0.468 |
|
| 2013 |
Harris RC, Boschitsch AH, Fenley MO. Influence of Grid Spacing in Poisson-Boltzmann Equation Binding Energy Estimation. Journal of Chemical Theory and Computation. 9: 3677-3685. PMID 23997692 DOI: 10.1021/Ct300765W |
0.434 |
|
| 2013 |
MacKoy T, Harris RC, Johnson J, Mascagni M, Fenley MO. Numerical optimization of a walk-on-spheres solver for the linear Poisson-Boltzmann equation Communications in Computational Physics. 13: 195-206. DOI: 10.4208/Cicp.220711.041011S |
0.435 |
|
| 2013 |
Harris RC, Mackoy T, Fenley MO. A Stochastic Solver of the Generalized Born Model Computational and Mathematical Biophysics. 1: 63-74. DOI: 10.2478/Mlbmb-2013-0003 |
0.489 |
|
| 2012 |
Kirmizialtin S, Silalahi AR, Elber R, Fenley MO. The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations. Biophysical Journal. 102: 829-38. PMID 22385854 DOI: 10.1016/J.Bpj.2011.12.055 |
0.444 |
|
| 2012 |
Harris RC, Fenley MO. A Stochastic Technique that Computes Electrostatic Solvation and Binding Free Energies in the Generalized Born Model with Exact Born Radii Biophysical Journal. 102: 168a-169a. DOI: 10.1016/J.Bpj.2011.11.916 |
0.515 |
|
| 2011 |
Boschitsch AH, Fenley MO. A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids. Journal of Chemical Theory and Computation. 7: 1524-1540. PMID 21984876 DOI: 10.1021/Ct1006983 |
0.416 |
|
| 2011 |
Fenley MO, Russo C, Manning GS. Theoretical assessment of the oligolysine model for ionic interactions in protein-DNA complexes. The Journal of Physical Chemistry. B. 115: 9864-72. PMID 21751805 DOI: 10.1021/Jp204915Y |
0.516 |
|
| 2011 |
Harris RC, Bredenberg JH, Silalahi AR, Boschitsch AH, Fenley MO. Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand-nucleic acid complexes. Biophysical Chemistry. 156: 79-87. PMID 21458909 DOI: 10.1016/J.Bpc.2011.02.010 |
0.518 |
|
| 2010 |
Silalahi AR, Boschitsch AH, Harris RC, Fenley MO. Comparing the Predictions of the Nonlinear Poisson-Boltzmann Equation and the Ion Size-Modified Poisson-Boltzmann Equation for a Low-Dielectric Charged Spherical Cavity in an Aqueous Salt Solution. Journal of Chemical Theory and Computation. 6: 3631-3639. PMID 22723750 DOI: 10.1021/Ct1002785 |
0.479 |
|
| 2010 |
Fenley MO, Harris RC, Jayaram B, Boschitsch AH. Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach. Biophysical Journal. 99: 879-86. PMID 20682266 DOI: 10.1016/J.Bpj.2010.04.066 |
0.527 |
|
| 2010 |
Fenley MO, Mascagni M, McClain J, Silalahi AR, Simonov NA. Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson-Boltzmann Equation Over a Broad Range of Salt Concentration. Journal of Chemical Theory and Computation. 6: 300-314. PMID 20640228 DOI: 10.1021/Ct9003806 |
0.503 |
|
| 2010 |
Russo C, Asbury E, Wall M, Fenley MO. Salt-Dependence of DNA-Protein Binding: A Study of Four DNA-Binding Families Biophysical Journal. 98: 41a. DOI: 10.1016/J.Bpj.2009.12.236 |
0.524 |
|
| 2009 |
Srinivasan AR, Sauers RR, Fenley MO, Boschitsch AH, Matsumoto A, Colasanti AV, Olson WK. Properties of the Nucleic-acid Bases in Free and Watson-Crick Hydrogen-bonded States: Computational Insights into the Sequence-dependent Features of Double-helical DNA. Biophysical Reviews. 1: 13-20. PMID 21218180 DOI: 10.1007/S12551-008-0003-2 |
0.465 |
|
| 2008 |
de Carvalho SJ, Fenley MO, da Silva FL. Protein-ion binding process on finite macromolecular concentration. A Poisson-Boltzmann and Monte Carlo study. The Journal of Physical Chemistry. B. 112: 16766-76. PMID 19368030 DOI: 10.1021/Jp800783X |
0.51 |
|
| 2008 |
Bredenberg JH, Russo C, Fenley MO. Salt-mediated electrostatics in the association of TATA binding proteins to DNA: a combined molecular mechanics/Poisson-Boltzmann study. Biophysical Journal. 94: 4634-45. PMID 18326635 DOI: 10.1529/Biophysj.107.125609 |
0.481 |
|
| 2008 |
Min D, Li H, Li G, Berg BA, Fenley MO, Yang W. Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method Chemical Physics Letters. 454: 391-395. DOI: 10.1016/J.Cplett.2008.02.055 |
0.439 |
|
| 2007 |
Simonov NA, Mascagni M, Fenley MO. Monte Carlo-based linear Poisson-Boltzmann approach makes accurate salt-dependent solvation free energy predictions possible. The Journal of Chemical Physics. 127: 185105. PMID 18020668 DOI: 10.1063/1.2803189 |
0.52 |
|
| 2007 |
Xu D, Landon T, Greenbaum NL, Fenley MO. The electrostatic characteristics of G.U wobble base pairs. Nucleic Acids Research. 35: 3836-47. PMID 17526525 DOI: 10.1093/Nar/Gkm274 |
0.587 |
|
| 2007 |
Boschitsch AH, Fenley MO. A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation. Journal of Computational Chemistry. 28: 909-21. PMID 17238171 DOI: 10.1002/Jcc.20565 |
0.503 |
|
| 2005 |
Xu D, Greenbaum NL, Fenley MO. Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features. Nucleic Acids Research. 33: 1154-61. PMID 15728744 DOI: 10.1093/Nar/Gki249 |
0.583 |
|
| 2005 |
Chapman MS, Fabiola F, Korostelev A, Fenley M. Refinement when amplitudes aren't enough: real-space, H-bonding and electrostatics Acta Crystallographica Section a Foundations of Crystallography. 61: c114-c115. DOI: 10.1107/S0108767305095176 |
0.202 |
|
| 2004 |
Korostelev A, Fenley MO, Chapman MS. Impact of a Poisson-Boltzmann electrostatic restraint on protein structures refined at medium resolution. Acta Crystallographica. Section D, Biological Crystallography. 60: 1786-94. PMID 15388925 DOI: 10.1107/S0907444904019110 |
0.479 |
|
| 2004 |
Aittaleb M, Visone T, Fenley MO, Li H. Structural and thermodynamic evidence for a stabilizing role of Nop5p in S-adenosyl-L-methionine binding to fibrillarin. The Journal of Biological Chemistry. 279: 41822-9. PMID 15286083 DOI: 10.1074/Jbc.M406209200 |
0.441 |
|
| 2004 |
Gattis JL, Ruben E, Fenley MO, Ellington WR, Chapman MS. The active site cysteine of arginine kinase: structural and functional analysis of partially active mutants. Biochemistry. 43: 8680-9. PMID 15236576 DOI: 10.1021/Bi049793I |
0.366 |
|
| 2004 |
Moore T, Zhang Y, Fenley MO, Li H. Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure (London, England : 1993). 12: 807-18. PMID 15130473 DOI: 10.1016/J.Str.2004.02.033 |
0.379 |
|
| 2004 |
Boschitsch AH, Fenley MO. Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation. Journal of Computational Chemistry. 25: 935-55. PMID 15027106 DOI: 10.1002/Jcc.20000 |
0.471 |
|
| 2002 |
Boschitsch AH, Fenley MO, Zhou H. Fast Boundary Element Method for the Linear Poisson−Boltzmann Equation The Journal of Physical Chemistry B. 106: 2741-2754. DOI: 10.1021/Jp013607Q |
0.439 |
|
| 2000 |
Fenley MO, Olson WK, Manning GS. Dependence of counterion binding on DNA shape as determined by counterion condensation theory Macromolecules. 33: 1899-1903. DOI: 10.1021/Ma990191U |
0.434 |
|
| 1999 |
Boschitsch AH, Fenley MO, Olson WK. A Fast Adaptive Multipole Algorithm for Calculating Screened Coulomb (Yukawa) Interactions Journal of Computational Physics. 151: 212-241. DOI: 10.1006/Jcph.1998.6176 |
0.376 |
|
| 1998 |
Fenley MO, Manning GS, Marky NL, Olson WK. Excess counterion binding and ionic stability of kinked and branched DNA. Biophysical Chemistry. 74: 135-52. PMID 9760723 DOI: 10.1016/S0301-4622(98)00171-9 |
0.401 |
|
| 1996 |
Fenley MO, Olson WK, Chua K, Boschitsch AH. Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA Journal of Computational Chemistry. 17: 976-991. DOI: 10.1002/(Sici)1096-987X(199606)17:8<976::Aid-Jcc7>3.0.Co;2-O |
0.394 |
|
| 1994 |
Fenley MO, Olson WK, Tobias I, Manning GS. Electrostatic effects in short superhelical DNA. Biophysical Chemistry. 50: 255-71. PMID 8011947 DOI: 10.1016/0301-4622(93)E0094-L |
0.375 |
|
| 1992 |
Fenley MO, Manning GS, Olson WK. Electrostatic persistence length of a smoothly bending polyion computed by numerical counterion condensation theory Journal of Physical Chemistry. 96: 3963-3969. DOI: 10.1021/J100189A011 |
0.47 |
|
| 1990 |
Fenley MO, Manning GS, Olson WK. A numerical counterion condensation analysis of the B-Z transition of DNA. Biopolymers. 30: 1205-13. PMID 2085658 DOI: 10.1002/Bip.360301306 |
0.401 |
|
| 1990 |
Fenley MO, Manning GS, Olson WK. Approach to the limit of counterion condensation. Biopolymers. 30: 1191-203. PMID 2085657 DOI: 10.1002/Bip.360301305 |
0.379 |
|
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