-
1
-
-
34248393495
-
Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling
-
10.1107/S0021889807001707
-
J. Lipfert, V. B. Chu, Y. Bai, D. Herschlag, and S. Doniach, "Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling,"J. Appl. Crystallogr. 40, s229-s234 (2007). 10.1107/S0021889807001707
-
(2007)
J. Appl. Crystallogr.
, vol.40
-
-
Lipfert, J.1
Chu, V.B.2
Bai, Y.3
Herschlag, D.4
Doniach, S.5
-
2
-
-
46749106335
-
Mono- and trivalent ions around DNA: A small-angle scattering study of competition and interactions
-
10.1529/biophysj.107.123174
-
K. Andresen, X. Qiu, S. A. Pabit, J. S. Lamb, H. Y. Park, L. W. Kwok, and L. Pollack, "Mono- and trivalent ions around DNA: A small-angle scattering study of competition and interactions,"Biophys. J. 95, 287-295 (2008). 10.1529/biophysj.107.123174
-
(2008)
Biophys. J.
, vol.95
, pp. 287-295
-
-
Andresen, K.1
Qiu, X.2
Pabit, S.A.3
Lamb, J.S.4
Park, H.Y.5
Kwok, L.W.6
Pollack, L.7
-
3
-
-
67651163671
-
Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA
-
10.1093/nar/gkp257
-
S. A. Pabit, X. Qiu, J. S. Lamb, L. Li, S. P. Meisburger, and L. Pollack, "Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA,"Nucl. Acids Res. 37, 3887-3896 (2009). 10.1093/nar/gkp257
-
(2009)
Nucl. Acids Res.
, vol.37
, pp. 3887-3896
-
-
Pabit, S.A.1
Qiu, X.2
Lamb, J.S.3
Li, L.4
Meisburger, S.P.5
Pollack, L.6
-
4
-
-
78649935315
-
Counting ions around DNA with anomalous small-angle X-ray scattering
-
10.1021/ja107259y
-
S. A. Pabit, S. P. Meisburger, J. S. Lamb, L. Li, J. M. Blose, C. D. Jones, and L. Pollack, "Counting ions around DNA with anomalous small-angle X-ray scattering,"J. Am. Chem. Soc. 132, 16334-16336 (2010). 10.1021/ja107259y
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 16334-16336
-
-
Pabit, S.A.1
Meisburger, S.P.2
Lamb, J.S.3
Li, L.4
Blose, J.M.5
Jones, C.D.6
Pollack, L.7
-
5
-
-
79955846859
-
SAXS studies of ion-nucleic acid interactions
-
10.1146/annurev-biophys-042910-155349
-
L. Pollack, "SAXS studies of ion-nucleic acid interactions, "Ann. Rev. Biophys. 40, 225-242 (2011). 10.1146/annurev-biophys-042910- 155349
-
(2011)
Ann. Rev. Biophys.
, vol.40
, pp. 225-242
-
-
Pollack, L.1
-
6
-
-
84857311171
-
RNA and its ionic cloud: Solution scattering experiments and atomically detailed simulations
-
10.1016/j.bpj.2012.01.013
-
S. Kirmizialtin, S. A. Pabit, S. P. Meisburger, L. Pollack, and R. Elber, "RNA and its ionic cloud: Solution scattering experiments and atomically detailed simulations,"Biophys. J. 102, 819-828 (2012). 10.1016/j.bpj.2012. 01.013
-
(2012)
Biophys. J.
, vol.102
, pp. 819-828
-
-
Kirmizialtin, S.1
Pabit, S.A.2
Meisburger, S.P.3
Pollack, L.4
Elber, R.5
-
7
-
-
36848999901
-
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
-
10.1021/ja075020g
-
Y. Bai, M. Greenfeld, K. J. Travers, V. B. Chu, J. Lipfert, S. Doniach, and D. Herschlag, "Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids,"J. Am. Chem. Soc. 129, 14981-14988 (2007). 10.1021/ja075020g
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 14981-14988
-
-
Bai, Y.1
Greenfeld, M.2
Travers, K.J.3
Chu, V.B.4
Lipfert, J.5
Doniach, S.6
Herschlag, D.7
-
8
-
-
36048952831
-
Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory
-
10.1529/biophysj.106.099168
-
V. B. Chu, Y. Bai, J. Lipfert, D. Herschlag, and S. Doniach, "Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory,"Biophys. J. 93, 3202-3209 (2007). 10.1529/biophysj.106.099168
-
(2007)
Biophys. J.
, vol.93
, pp. 3202-3209
-
-
Chu, V.B.1
Bai, Y.2
Lipfert, J.3
Herschlag, D.4
Doniach, S.5
-
9
-
-
57649130782
-
A repulsive field: Advances in the electrostatics of the ion atmosphere
-
10.1016/j.cbpa.2008.10.010
-
V. B. Chu, Y. Bai, J. Lipfert, D. Herschlag, and S. Doniach, "A repulsive field: Advances in the electrostatics of the ion atmosphere, "Curr. Opin. Chem. Biol. 12, 619-625 (2008). 10.1016/j.cbpa.2008.10.010
-
(2008)
Curr. Opin. Chem. Biol.
, vol.12
, pp. 619-625
-
-
Chu, V.B.1
Bai, Y.2
Lipfert, J.3
Herschlag, D.4
Doniach, S.5
-
10
-
-
67649363284
-
Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop
-
10.1016/j.jmb.2009.05.071
-
A. A. Chen, D. E. Draper, and R. V. Pappu, "Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop,"J. Mol. Biol. 390, 805-819 (2009). 10.1016/j.jmb.2009.05.071
-
(2009)
J. Mol. Biol.
, vol.390
, pp. 805-819
-
-
Chen, A.A.1
Draper, D.E.2
Pappu, R.V.3
-
11
-
-
84857256519
-
The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations
-
10.1016/j.bpj.2011.12.055
-
S. Kirmizialtin, A. R. J. Silalahi, R. Elber, and M. O. Fenley, "The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations,"Biophys. J. 102, 829-838 (2012). 10.1016/j.bpj.2011.12.055
-
(2012)
Biophys. J.
, vol.102
, pp. 829-838
-
-
Kirmizialtin, S.1
Silalahi, A.R.J.2
Elber, R.3
Fenley, M.O.4
-
12
-
-
67649359324
-
The influence of monovalent cation size on the stability of RNA tertiary structures
-
10.1016/j.jmb.2009.04.083
-
D. Lambert, D. Leipply, R. Shiman, and D. E. Draper, "The influence of monovalent cation size on the stability of RNA tertiary structures,"J. Mol. Biol. 390, 791-804 (2009). 10.1016/j.jmb.2009.04.083
-
(2009)
J. Mol. Biol.
, vol.390
, pp. 791-804
-
-
Lambert, D.1
Leipply, D.2
Shiman, R.3
Draper, D.E.4
-
13
-
-
79953907770
-
Monovalent cation size and DNA conformational stability
-
10.1021/bi1015524
-
E. Stellwagen, J. M. Muse, and N. C. Stellwagen, "Monovalent cation size and DNA conformational stability,"Biochemistry 50, 3084-3094 (2011). 10.1021/bi1015524
-
(2011)
Biochemistry
, vol.50
, pp. 3084-3094
-
-
Stellwagen, E.1
Muse, J.M.2
Stellwagen, N.C.3
-
14
-
-
84858228831
-
Electrostatics of nucleic acid folding under conformational constraint
-
10.1021/ja208466h
-
P. C. Anthony, A. Y. L. Sim, V. B. Chu, S. Doniach, S. M. Block, and D. Herschlag, "Electrostatics of nucleic qcid folding under conformationa| constraint,"J. Am. Chem. Soc. 134, 4607-4614 (2012). 10.1021/ja208466h
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 4607-4614
-
-
Anthony, P.C.1
Sim, A.Y.L.2
Chu, V.B.3
Doniach, S.4
Block, S.M.5
Herschlag, D.6
-
15
-
-
0030127818
-
A simple statistical mechanical0approach to the free energy of the electric double layer includyng the excluded volume effect
-
10.1051/jp2:1996193
-
V. Kralj-Iglic and A. Iglic, "A simple statistical mechanical approach to the free energy of the electric double layer including the excluded volume effect,"J. Phys. II 6, 477-491 (1996). 10.1051/jp2:1996193
-
(1996)
J. Phys. II
, vol.6
, pp. 477-491
-
-
Kralj-Iglic, V.1
Iglic, A.2
-
16
-
-
6244273869
-
Steric effects in electrolytes: A modified Poisson-Boltzmann equation
-
10.1103/PhysRevLett.79.435
-
I. Borukhov, D. Andelman, and H. Orland, "Steric effects in electrolytes: A modified Poisson-Boltzmann equation,"Phys. Rev. Lett. 79, 435-438 (1997). 10.1103/PhysRevLett.79.435
-
(1997)
Phys. Rev. Lett.
, vol.79
, pp. 435-438
-
-
Borukhov, I.1
Andelman, D.2
Orland, H.3
-
17
-
-
0037173269
-
Lattice site exclusion effect on the double layer interaction
-
10.1021/la020194r
-
M. Manciu and E. Ruckenstein, "Lattice site exclusion effect on the double layer interaction,"Langmuir 18, 5178-5185 (2002). 10.1021/la020194r
-
(2002)
Langmuir
, vol.18
, pp. 5178-5185
-
-
Manciu, M.1
Ruckenstein, E.2
-
18
-
-
0001020827
-
Beyond Poisson-Boltzmann: Fluctuation effects and correlation functions
-
10.1007/s101890050023
-
R. R. Netz and H. Orland, "Beyond Poisson-Boltzmann: Fluctuation effects and correlation functions,"Eur. Phys. J. E 1, 203-214 (2000). 10.1007/s101890050023
-
(2000)
Eur. Phys. J. e
, vol.1
, pp. 203-214
-
-
Netz, R.R.1
Orland, H.2
-
19
-
-
78651328563
-
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
-
10.1021/ct1002785
-
A. R. J. Silalahi, A. H. Boschitsch, R. C. Harris, and M. O. Fenley, "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,"J. Chem. Theory Comput. 6, 3631-3639 (2010). 10.1021/ct1002785
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3631-3639
-
-
Silalahi, A.R.J.1
Boschitsch, A.H.2
Harris, R.C.3
Fenley, M.O.4
-
20
-
-
80051618654
-
Mean-field description of ionic size effects with nonuniform ionic sizes: A numerical approach
-
10.1103/PhysRevE.84.021901
-
S. Zhou, Z. Wong, and B. Li, "Mean-field description of ionic size effects with nonuniform ionic sizes: A numerical approach,"Phys. Rev. E 84, 021901 (2011). 10.1103/PhysRevE.84.021901
-
(2011)
Phys. Rev. e
, vol.84
, pp. 021901
-
-
Zhou, S.1
Wong, Z.2
Li, B.3
-
21
-
-
84859110300
-
Formulation of a new and simple nonuniform size-modified Poisson-Boltzmann description
-
10.1002/jcc.22946
-
A. H. Boschitsch and P. V. Danilov, "Formulation of a new and simple nonuniform size-modified Poisson-Boltzmann description,"J. Comput. Chem. 33, 1152-1164 (2012). 10.1002/jcc.22946
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 1152-1164
-
-
Boschitsch, A.H.1
Danilov, P.V.2
-
22
-
-
77955695135
-
Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach
-
10.1016/j.bpj.2010.04.066
-
M. O. Fenley, R. C. Harris, B. Jayaram, and A. H. Boschitsch, "Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach,"Biophys. J. 99, 879-886 (2010). 10.1016/j.bpj.2010.04.066
-
(2010)
Biophys. J.
, vol.99
, pp. 879-886
-
-
Fenley, M.O.1
Harris, R.C.2
Jayaram, B.3
Boschitsch, A.H.4
-
23
-
-
80051726307
-
Theoretical assessment of the oligolysine model for ionic interactions in protein DNA complexes
-
10.1021/jp204915y
-
M. O. Fenley, C. Russo, and G. S. Manning, "Theoretical assessment of the oligolysine model for ionic interactions in protein DNA complexes,"J. Phys. Chem. B 115, 9864-9872 (2011). 10.1021/jp204915y
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 9864-9872
-
-
Fenley, M.O.1
Russo, C.2
Manning, G.S.3
-
24
-
-
79955888291
-
Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand-nucleic acid complexes
-
10.1016/j.bpc.2011.02.010
-
R. C. Harris, J. H. Bredenberg, A. R. J. Silalahi, A. H. Boschitsch, and M. O. Fenley, "Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand-nucleic acid complexes,"Biophys. Chem. 156, 79-87 (2011). 10.1016/j.bpc.2011.02.010
-
(2011)
Biophys. Chem.
, vol.156
, pp. 79-87
-
-
Harris, R.C.1
Bredenberg, J.H.2
Silalahi, A.R.J.3
Boschitsch, A.H.4
Fenley, M.O.5
-
25
-
-
0026730188
-
Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan
-
10.1021/bi00152a033
-
D. P. Mascotti and T. M. Lohmann, "Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan,"Biochemistry 31, 8932-8946 (1992). 10.1021/bi00152a033
-
(1992)
Biochemistry
, vol.31
, pp. 8932-8946
-
-
Mascotti, D.P.1
Lohmann, T.M.2
-
26
-
-
0026619551
-
Poisson Boltzmann analysis of the λ repressor operator interaction
-
10.1016/S0006-3495(92)81723-X
-
M. Zacharias, B. A. Luty, M. E. Davis, and J. A. McCammon, "Poisson Boltzmann analysis of the λ repressor operator interaction,"Biophys. J. 63, 1280-1285 (1992). 10.1016/S0006-3495(92)81723-X
-
(1992)
Biophys. J.
, vol.63
, pp. 1280-1285
-
-
Zacharias, M.1
Luty, B.A.2
Davis, M.E.3
McCammon, J.A.4
-
27
-
-
0027379588
-
Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan
-
10.1021/bi00091a006
-
D. P. Mascotti and T. M. Lohmann, "Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan, "Biochemistry 32, 10568-10579 (1993). 10.1021/bi00091a006
-
(1993)
Biochemistry
, vol.32
, pp. 10568-10579
-
-
Mascotti, D.P.1
Lohmann, T.M.2
-
28
-
-
0028246710
-
Salt effects on ligand-DNA binding: Minor groove binding antibiotics
-
10.1006/jmbi.1994.1285
-
V. K. Misra, K. A. Sharp, R. A. Friedman, and B. Honig, "Salt effects on ligand-DNA binding: Minor groove binding antibiotics,"J. Mol. Biol. 238, 245-263 (1994). 10.1006/jmbi.1994.1285
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 245-263
-
-
Misra, V.K.1
Sharp, K.A.2
Friedman, R.A.3
Honig, B.4
-
29
-
-
0028239626
-
Salt effects on protein DNA interactions: The λ cI repressor and EcoRI endonuclease
-
10.1006/jmbi.1994.1286
-
V. K. Misra, J. L. Hecht, K. A. Sharp, R. A. Friedman, and B. Honig, "Salt effects on protein DNA interactions: The λ cI repressor and EcoRI endonuclease,"J. Mol. Biol. 238, 264-280 (1994). 10.1006/jmbi.1994. 1286
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 264-280
-
-
Misra, V.K.1
Hecht, J.L.2
Sharp, K.A.3
Friedman, R.A.4
Honig, B.5
-
30
-
-
0029047968
-
On the magnitude of the electrostatic contribution to ligand DNA interactions
-
10.1073/pnas.92.10.4691
-
V. K. Misra and B. Honig, "On the magnitude of the electrostatic contribution to ligand DNA interactions,"Proc. Natl. Acad. Sci. U.S.A. 92, 4691-4695 (1995). 10.1073/pnas.92.10.4691
-
(1995)
Proc. Natl. Acad. Sci. U.S.A.
, vol.92
, pp. 4691-4695
-
-
Misra, V.K.1
Honig, B.2
-
31
-
-
0029782652
-
Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR
-
10.1021/bi9607259
-
P. C. Bevilacqua, and T. R. Cech, "Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR,"Biochemistry 35, 9983-9994 (1996). 10.1021/bi9607259
-
(1996)
Biochemistry
, vol.35
, pp. 9983-9994
-
-
Bevilacqua, P.C.1
Cech, T.R.2
-
32
-
-
0030920231
-
Thermodynamics of oligoarginines binding to RNA and DNA
-
10.1021/bi970272n
-
D. P. Mascotti and T. M. Lohmann, "Thermodynamics of oligoarginines binding to RNA and DNA,"Biochemistry 36, 7272-7279 (1997). 10.1021/bi970272n
-
(1997)
Biochemistry
, vol.36
, pp. 7272-7279
-
-
Mascotti, D.P.1
Lohmann, T.M.2
-
33
-
-
0034695428
-
Contributions of basic residues to ribosomal protein L11 recognition of RNA
-
10.1006/jmbi.1999.3372
-
D. GuhaThakurta and D. E. Draper, "Contributions of basic residues to ribosomal protein L11 recognition of RNA,"J. Mol. Biol. 295, 569-580 (2000). 10.1006/jmbi.1999.3372
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 569-580
-
-
Guhathakurta, D.1
Draper, D.E.2
-
34
-
-
0037129948
-
Thermodynamics of aminoglycoside-rRNA recognition: The binding of neomycin-class aminoglycosides to the A site of 16S rRNA
-
10.1021/bi020130f
-
M. Kaul and D. S. Pilch, "Thermodynamics of aminoglycoside-rRNA recognition: The binding of neomycin-class aminoglycosides to the A site of 16S rRNA,"Biochemistry 41, 7695-7706 (2002). 10.1021/bi020130f
-
(2002)
Biochemistry
, vol.41
, pp. 7695-7706
-
-
Kaul, M.1
Pilch, D.S.2
-
35
-
-
0038499698
-
Electrostatic interactions in a peptide-RNA complex
-
10.1016/S0022-2836(03)00615-6
-
C. García-García and D. E. Draper, "Electrostatic interactions in a peptide-RNA complex,"J. Mol. Biol. 331, 75-88 (2003). 10.1016/S0022-2836(03)00615-6
-
(2003)
J. Mol. Biol.
, vol.331
, pp. 75-88
-
-
García-García, C.1
Draper, D.E.2
-
36
-
-
39149124468
-
Interplay of ion binding and attraction in DNA condensed by multivalent cations
-
10.1093/nar/gkm1038
-
B. A. Todd and D. C. Rau, "Interplay of ion binding and attraction in DNA condensed by multivalent cations,"Nucl. Acids Res. 36, 501-510 (2008). 10.1093/nar/gkm1038
-
(2008)
Nucl. Acids Res.
, vol.36
, pp. 501-510
-
-
Todd, B.A.1
Rau, D.C.2
-
37
-
-
67650542563
-
Contribution of the closing base pair to exceptional stability in RNA tetraloops: Roles for molecular mimicry and electrostatic factors
-
10.1021/ja900065e
-
J. M. Blose, D. J. Proctor, N. Veeraraghavan, V. K. Misra, and P. C. Bevilacqua, "Contribution of the closing base pair to exceptional stability in RNA tetraloops: Roles for molecular mimicry and electrostatic factors,"J. Am. Chem. Soc. 131, 8474-8484 (2009). 10.1021/ja900065e
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 8474-8484
-
-
Blose, J.M.1
Proctor, D.J.2
Veeraraghavan, N.3
Misra, V.K.4
Bevilacqua, P.C.5
-
38
-
-
60649106752
-
RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloid coralyne
-
10.1039/b816480k
-
M. M. Islam, P. Pandya, S. Kumar, and G. S. Kumar, "RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloid coralyne,"Mol. Biosyst. 5, 244-254 (2009). 10.1039/b816480k
-
(2009)
Mol. Biosyst.
, vol.5
, pp. 244-254
-
-
Islam, M.M.1
Pandya, P.2
Kumar, S.3
Kumar, G.S.4
-
39
-
-
61949239352
-
Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides
-
10.1021/jp806597w
-
M. M. Islam, S. R. Chowdhury, and G. S. Kumar, "Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides,"J. Phys. Chem. B 113, 1210-1224 (2009). 10.1021/jp806597w
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 1210-1224
-
-
Islam, M.M.1
Chowdhury, S.R.2
Kumar, G.S.3
-
40
-
-
75349085366
-
A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation
-
10.1093/nar/gkp683
-
N. Korolev, N. V. Berezhnoy, K. D. Eom, J. P. Tam, and L. Nordenskiold, "A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation,"Nucl. Acids Res. 37, 7137-7150 (2009). 10.1093/nar/gkp683
-
(2009)
Nucl. Acids Res.
, vol.37
, pp. 7137-7150
-
-
Korolev, N.1
Berezhnoy, N.V.2
Eom, K.D.3
Tam, J.P.4
Nordenskiold, L.5
-
41
-
-
70349422115
-
Thermodynamic profiling of HIV RREIIB RNA-zinc finger interactions
-
10.1016/j.jmb.2009.07.066
-
S. H. Mishra, A. M. Spring, and M. W. Germann, "Thermodynamic profiling of HIV RREIIB RNA-zinc finger interactions,"J. Mol. Biol. 393, 369-382 (2009). 10.1016/j.jmb.2009.07.066
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 369-382
-
-
Mishra, S.H.1
Spring, A.M.2
Germann, M.W.3
-
42
-
-
77951674873
-
Effects of the nature and concentration of salt on the interaction of the HIV-1 nucleocapsid protein with SL3 RNA
-
10.1021/bi901279e
-
S. S. Athavale, W. Ouyang, M. P. McPike, B. S. Hudson, and P. N. Borer, "Effects of the nature and concentration of salt on the interaction of the HIV-1 nucleocapsid protein with SL3 RNA,"Biochemistry 49, 3525-3533 (2010). 10.1021/bi901279e
-
(2010)
Biochemistry
, vol.49
, pp. 3525-3533
-
-
Athavale, S.S.1
Ouyang, W.2
McPike, M.P.3
Hudson, B.S.4
Borer, P.N.5
-
43
-
-
77449117999
-
Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB
-
10.1074/jbc.M109.081380
-
A. Paleskava, A. L. Konevega, and M. V. Rodnina, "Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB,"J. Biol. Chem. 285, 3014-3020 (2010). 10.1074/jbc.M109.081380
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 3014-3020
-
-
Paleskava, A.1
Konevega, A.L.2
Rodnina, M.V.3
-
44
-
-
77956064643
-
Thermodynamics of peptide-RNA recognition: The binding of a Tat peptide to TAR RNA
-
10.1021/jp1000545
-
H. Suryawanshi, H. Sabharwal, and S. Maiti, "Thermodynamics of peptide-RNA recognition: The binding of a Tat peptide to TAR RNA,"J. Phys. Chem. B 114, 11155-11163 (2010). 10.1021/jp1000545
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 11155-11163
-
-
Suryawanshi, H.1
Sabharwal, H.2
Maiti, S.3
-
45
-
-
77749253818
-
An RNA aptamer with high affinity and broad specificity for zinc finger proteins
-
10.1021/bi9016654
-
T. C. Weiss, G. G. Zhai, S. S. Bhatia, and P. J. Romaniuk, "An RNA aptamer with high affinity and broad specificity for zinc finger proteins,"Biochemistry 49, 2732-2740 (2010). 10.1021/bi9016654
-
(2010)
Biochemistry
, vol.49
, pp. 2732-2740
-
-
Weiss, T.C.1
Zhai, G.G.2
Bhatia, S.S.3
Romaniuk, P.J.4
-
46
-
-
77953106274
-
Coevolution of Drosophila snf protein and its snRNA targets
-
10.1021/bi100374d
-
S. G. Williams and K. B. Hall, "Coevolution of Drosophila snf protein and its snRNA targets,"Biochemistry 49, 4571-4582 (2010). 10.1021/bi100374d
-
(2010)
Biochemistry
, vol.49
, pp. 4571-4582
-
-
Williams, S.G.1
Hall, K.B.2
-
47
-
-
77951023778
-
Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices
-
10.1016/j.biochi.2010.02.004
-
H. Xi, S. Kumar, L. Dosen-Micovic, and D. P. Arya, "Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices,"Biochimie 92, 514-529 (2010). 10.1016/j.biochi.2010.02.004
-
(2010)
Biochimie
, vol.92
, pp. 514-529
-
-
Xi, H.1
Kumar, S.2
Dosen-Micovic, L.3
Arya, D.P.4
-
48
-
-
0017146579
-
Ion effects on ligand-nucleic acid interactions
-
10.1016/S0022-2836(76)80023-X
-
M. T. Record Jr., T. M. Lohman, and P. de Haseth, "Ion effects on ligand-nucleic acid interactions,"J. Mol. Biol. 107, 145-158 (1976). 10.1016/S0022-2836(76)80023-X
-
(1976)
J. Mol. Biol.
, vol.107
, pp. 145-158
-
-
Record, Jr.M.T.1
Lohman, T.M.2
De Haseth, P.3
-
49
-
-
0031776135
-
Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: A practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts
-
10.1016/S0065-3233(08)60655-5
-
M. T. Record Jr., W. Zhang, and C. F. Anderson, "Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: A practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts,"Adv. Protein Chem. 51, 281-353 (1998). 10.1016/S0065-3233(08)60655-5
-
(1998)
Adv. Protein Chem.
, vol.51
, pp. 281-353
-
-
Record, Jr.M.T.1
Zhang, W.2
Anderson, C.F.3
-
50
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
10.1093/nar/gkg680
-
L. Xiang-Jun and W. K. Olson, "3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures,"Nucl. Acids Res. 31, 5108-5121 (2003). 10.1093/nar/gkg680
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 5108-5121
-
-
Xiang-Jun, L.1
Olson, W.K.2
-
51
-
-
50349085962
-
3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
-
10.1038/nprot.2008.104
-
L. Xiang-Jun and W. K. Olson, "3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures,"Nat. Protoc. 3, 1213-1227 (2008). 10.1038/nprot.2008.104
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1213-1227
-
-
Xiang-Jun, L.1
Olson, W.K.2
-
52
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
10.1021/ja00124a002
-
W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, "A second generation force field for the simulation of proteins, nucleic acids, and organic molecules,"J. Am. Chem. Soc. 117, 5179-5197 (1995). 10.1021/ja00124a002
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
53
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup of Poisson Boltzmann electrostatics calculations
-
10.1093/nar/gkh381
-
T. J. Dolinsky, J. E. Nielsen, J. A. McCammon, and N. A. Baker, "PDB2PQR: An automated pipeline for the setup of Poisson Boltzmann electrostatics calculations,"Nucl. Acids Res. 32, W665-W667 (2004). 10.1093/nar/gkh381
-
(2004)
Nucl. Acids Res.
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
54
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
10.1093/nar/gkm276
-
T. J. Dolinsky, P. Czodrowski, H. Li, J. E. Nielsen, J. H. Jensen, G. Klebe, and N. A. Baker, "PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations,"Nucl. Acids Res. 35, W522-W525 (2007). 10.1093/nar/gkm276
-
(2007)
Nucl. Acids Res.
, vol.35
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
Baker, N.A.7
-
55
-
-
0033757806
-
The protein data bank and the challenge of structural genomics
-
10.1038/80734
-
H. M. Berman, T. N. Bhat, P. E. Bourne, Z. Feng, G. Gilliland, H. Weissig, and J. Westbrook, "The protein data bank and the challenge of structural genomics,"Nat. Struct. Mol. Biol. 7, 957-959 (2000). 10.1038/80734
-
(2000)
Nat. Struct. Mol. Biol.
, vol.7
, pp. 957-959
-
-
Berman, H.M.1
Bhat, T.N.2
Bourne, P.E.3
Feng, Z.4
Gilliland, G.5
Weissig, H.6
Westbrook, J.7
-
56
-
-
0024828309
-
The structure of DAPI bound to DNA
-
10.1080/07391102.1989.10508505
-
T. A. Larsen, D. S. Goodsell, D. Cascio, K. Grzeskowiak, and R. E. Dickerson, "The structure of DAPI bound to DNA,"J. Biomol. Struct. Dyn. 7, 477-491 (1989). 10.1080/07391102.1989.10508505
-
(1989)
J. Biomol. Struct. Dyn.
, vol.7
, pp. 477-491
-
-
Larsen, T.A.1
Goodsell, D.S.2
Cascio, D.3
Grzeskowiak, K.4
Dickerson, R.E.5
-
57
-
-
0026475822
-
Structural consequences of a carcinogenic alkylation lesion on DNA: Effect of O6-ethylguanine on the molecular structure of the d(CGC[e6G]AATTCGCG)- netropsin complex
-
10.1021/bi00162a022
-
M. Sriram, G. A. van der Marel, H. L. Roelen, J. H. van Boom, and A. H. Wang, "Structural consequences of a carcinogenic alkylation lesion on DNA: Effect of O6-ethylguanine on the molecular structure of the d(CGC[e6G]AATTCGCG)- netropsin complex,"Biochemistry 31, 11823-11834 (1992). 10.1021/bi00162a022
-
(1992)
Biochemistry
, vol.31
, pp. 11823-11834
-
-
Sriram, M.1
Van Der Marel, G.A.2
Roelen, H.L.3
Van Boom, J.H.4
Wang, A.H.5
-
58
-
-
0034616955
-
A thermodynamic and structural analysis of DNA minor-groove complex formation
-
10.1006/jmbi.2000.3869
-
S. Mazur, F. A. Tanious, D. Ding, A. Kumar, D. W. Boykin, I. J. Simpson, S. Neidle, and W. D. Wilson, "A thermodynamic and structural analysis of DNA minor-groove complex formation,"J. Mol. Biol. 300, 321-337 (2000). 10.1006/jmbi.2000.3869
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 321-337
-
-
Mazur, S.1
Tanious, F.A.2
Ding, D.3
Kumar, A.4
Boykin, D.W.5
Simpson, I.J.6
Neidle, S.7
Wilson, W.D.8
-
59
-
-
0029928846
-
A crystallographic and spectroscopic study of the complex between d(CGCGAATTCGCG)2 and 2,5-bis(4-guanylphenyl)furan, an analogue of berenil. Structural origins of enhanced DNA-binding affinity
-
10.1021/bi952162r
-
C. A. Laughton, F. Tanious, C. M. Nunn, D. W. Boykin, W. D. Wilson, and S. Neidle, "A crystallographic and spectroscopic study of the complex between d(CGCGAATTCGCG)2 and 2,5-bis(4-guanylphenyl)furan, an analogue of berenil. Structural origins of enhanced DNA-binding affinity,"Biochemistry 35, 5655-5661 (1996). 10.1021/bi952162r
-
(1996)
Biochemistry
, vol.35
, pp. 5655-5661
-
-
Laughton, C.A.1
Tanious, F.2
Nunn, C.M.3
Boykin, D.W.4
Wilson, W.D.5
Neidle, S.6
-
60
-
-
0030936234
-
Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin
-
10.1021/bi9628228
-
C. M. Nunn, E. Garman, and S. Neidle, "Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin,"Biochemistry 36, 4792-4799 (1997). 10.1021/bi9628228
-
(1997)
Biochemistry
, vol.36
, pp. 4792-4799
-
-
Nunn, C.M.1
Garman, E.2
Neidle, S.3
-
61
-
-
79955915303
-
A fast and robust Poisson-Boltzmann solver based on adaptive Cartesian grids
-
10.1021/ct1006983
-
A. H. Boschitsch and M. O. Fenley, "A fast and robust Poisson-Boltzmann solver based on adaptive Cartesian grids,"J. Chem. Theory Comput. 7, 1524-1540 (2011). 10.1021/ct1006983
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1524-1540
-
-
Boschitsch, A.H.1
Fenley, M.O.2
-
62
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic acids
-
10.1126/science.6879170
-
M. L. Connolly, "Solvent-accessible surfaces of proteins and nucleic acids,"Science 221, 709-713 (1983). 10.1126/science.6879170
-
(1983)
Science
, vol.221
, pp. 709-713
-
-
Connolly, M.L.1
-
64
-
-
0038650855
-
Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar
-
10.1016/S0006-3495(03)74453-1
-
F. Dong, M. Vijayakumar, and H. X. Zhou, "Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar,"Biophys. J. 85, 49-60 (2003). 10.1016/S0006-3495(03)74453-1
-
(2003)
Biophys. J.
, vol.85
, pp. 49-60
-
-
Dong, F.1
Vijayakumar, M.2
Zhou, H.X.3
-
65
-
-
33748261419
-
Electrostatic contribution to the binding stability of protein-protein complexes
-
10.1002/prot.21070
-
F. Dong and H. X. Zhou, "Electrostatic contribution to the binding stability of protein-protein complexes,"Proteins: Struct., Funct., Bioinf. 65, 87-102 (2006). 10.1002/prot.21070
-
(2006)
Proteins: Struct., Funct., Bioinf.
, vol.65
, pp. 87-102
-
-
Dong, F.1
Zhou, H.X.2
-
66
-
-
40549134985
-
Electrostatic rate enhancement and transient complex of protein protein association
-
10.1002/prot.21679
-
R. Alsallaq and H. X. Zhou, "Electrostatic rate enhancement and transient complex of protein protein association,"Proteins: Struct., Funct., Bioinf. 71, 320-335 (2008). 10.1002/prot.21679
-
(2008)
Proteins: Struct., Funct., Bioinf.
, vol.71
, pp. 320-335
-
-
Alsallaq, R.1
Zhou, H.X.2
-
67
-
-
33644594508
-
Coupling nonpolar and polar solvation free energies in implicit solvent models
-
10.1063/1.2171192
-
J. Dzubiella, J. M. J. Swanson, and J. A. McCammon, "Coupling nonpolar and polar solvation free energies in implicit solvent models,"J. Chem. Phys. 124, 084905 (2006). 10.1063/1.2171192
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 084905
-
-
Dzubiella, J.1
Swanson, J.M.J.2
McCammon, J.A.3
-
68
-
-
34548378695
-
Application of the level-set method to the implicit solvation of nonpolar molecules
-
10.1063/1.2757169
-
L. T. Cheng, J. Dzubiella, J. A. McCammon, and B. Li, "Application of the level-set method to the implicit solvation of nonpolar molecules,"J. Chem. Phys. 127, 084503 (2007). 10.1063/1.2757169
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 084503
-
-
Cheng, L.T.1
Dzubiella, J.2
McCammon, J.A.3
Li, B.4
-
69
-
-
70350482625
-
Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach
-
10.1063/1.3242274
-
L. T. Cheng, Z. Wang, P. Setny, J. Dzubiella, B. Li, and J. A. McCammon, "Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach,"J. Chem. Phys. 131, 144102 (2009). 10.1063/1.3242274
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 144102
-
-
Cheng, L.T.1
Wang, Z.2
Setny, P.3
Dzubiella, J.4
Li, B.5
McCammon, J.A.6
-
70
-
-
77956414486
-
Differential geometry based solvation model I: Eulerian formulation
-
10.1016/j.jc2010.06.036
-
Z. Chen, N. A. Baker, and G. W. Wei, "Differential geometry based solvation model I: Eulerian formulation,"J. Comput. Phys. 229, 8231-8258 (2010). 10.1016/j.jcp.2010.06.036
-
(2010)
J. Comput. Phys.
, vol.229
, pp. 8231-8258
-
-
Chen, Z.1
Baker, N.A.2
Wei, G.W.3
-
71
-
-
81455139588
-
Differential geometry based solvation model II: Lagrangian formulation
-
10.1007/s00285-011-0402-z
-
Z. Chen, N. A. Baker, and G. W. Wei, "Differential geometry based solvation model II: Lagrangian formulation,"J. Math. Biol. 63, 1139-1200 (2011). 10.1007/s00285-011-0402-z
-
(2011)
J. Math. Biol.
, vol.63
, pp. 1139-1200
-
-
Chen, Z.1
Baker, N.A.2
Wei, G.W.3
-
72
-
-
0000779818
-
Poisson-Boltzmann analytical gradients for molecular modeling calculations
-
10.1021/jp982513m
-
M. Friedrichs, R. Zhou, S. R. Edinger, and R. A. Friesner, "Poisson-Boltzmann analytical gradients for molecular modeling calculations,"J. Phys. Chem. B 103, 3057-3061 (1999). 10.1021/jp982513m
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 3057-3061
-
-
Friedrichs, M.1
Zhou, R.2
Edinger, S.R.3
Friesner, R.A.4
-
73
-
-
0035971738
-
A smooth permittivity function for Poisson Boltzmann solvation methods
-
10.1002/jcc.1032
-
J. A. Grant, B. T. Pickup, and A. Nicholls, "A smooth permittivity function for Poisson Boltzmann solvation methods,"J. Comput. Chem. 22, 608-640 (2001). 10.1002/jcc.1032
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 608-640
-
-
Grant, J.A.1
Pickup, B.T.2
Nicholls, A.3
-
74
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
10.1016/0022-2836(71)90324-X
-
B. Lee and F. M. Richards, "The interpretation of protein structures: Estimation of static accessibility,"J. Mol. Biol. 55, 379-400 (1971). 10.1016/0022-2836(71)90324-X
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
|