-
2
-
-
0030905954
-
Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: A quantum-chemical study
-
S? poner, J., Gabb, H.A., Leszczynski, J. and Hobza, P. (1997) Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study. Biophys. J., 73, 76-87.
-
(1997)
Biophys. J.
, vol.73
, pp. 76-87
-
-
Sponer, J.1
Gabb, H.A.2
Leszczynski, J.3
Hobza, P.4
-
3
-
-
69849114530
-
Classification and energetics of the base-phosphate interactions in RNA
-
Zirbel, C.L., Sponer, J.E., Sponer, J., Stombaugh, J. and Leontis, N.B. (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4898-4918
-
-
Zirbel, C.L.1
Sponer, J.E.2
Sponer, J.3
Stombaugh, J.4
Leontis, N.B.5
-
4
-
-
84867973569
-
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
-
Sponer, J., Mladek, A., Sponer, J.E., Svozil, D., Zgarbova, M., Banas, P., Jurecka, P. and Otyepka, M. (2012) The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys. Chem. Chem. Phys., 14, 15257-15277.
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 15257-15277
-
-
Sponer, J.1
Mladek, A.2
Sponer, J.E.3
Svozil, D.4
Zgarbova, M.5
Banas, P.6
Jurecka, P.7
Otyepka, M.8
-
5
-
-
0002594455
-
Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
-
S poner, J., Leszczynski, J. and Hobza, P. (2001) Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers, 61, 3-31.
-
(2001)
Biopolymers
, vol.61
, pp. 3-31
-
-
Sponer, J.1
-
6
-
-
43449137856
-
Nature and magnitude of aromatic stacking of nucleic acid bases
-
Sponer, J., Riley, K.E. and Hobza, P. (2008) Nature and magnitude of aromatic stacking of nucleic acid bases. Phys. Chem. Chem. Phys., 10, 2595-2610.
-
(2008)
Phys. Chem. Chem. Phys.
, vol.10
, pp. 2595-2610
-
-
Sponer, J.1
Riley, K.E.2
Hobza, P.3
-
7
-
-
0035010211
-
Geometric nomenclature and classification of RNA base pairs
-
Leontis, N.B. and Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
-
(2001)
RNA
, vol.7
, pp. 499-512
-
-
Leontis, N.B.1
Westhof, E.2
-
8
-
-
0037102491
-
The non-Watson-Crick base pairs and their associated isostericity matrices
-
Leontis, N.B., Stombaugh, J. and Westhof, E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497-3531.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3497-3531
-
-
Leontis, N.B.1
Stombaugh, J.2
Westhof, E.3
-
9
-
-
65549163541
-
Frequency and isostericity of RNA base pairs
-
Stombaugh, J., Zirbel, C.L., Westhof, E. and Leontis, N.B. (2009) Frequency and isostericity of RNA base pairs. Nucleic Acids Res., 37, 2294-2312.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2294-2312
-
-
Stombaugh, J.1
Zirbel, C.L.2
Westhof, E.3
Leontis, N.B.4
-
10
-
-
0034316780
-
Water-mediated base pairs in RNA: A quantum-chemical study
-
Brandl, M., Meyer, M. and Suhnel, J. (2000) Water-mediated base pairs in RNA: a quantum-chemical study. J. Phys. Chem. A, 104, 11177-11187.
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 11177-11187
-
-
Brandl, M.1
Meyer, M.2
Suhnel, J.3
-
11
-
-
79951544368
-
Protonation of base pairs in RNA: Context analysis and quantum chemical investigations of their geometries and stabilities
-
Chawla, M., Sharma, P., Halder, S., Bhattacharyya, D. and Mitra, A. (2011) Protonation of base pairs in RNA: context analysis and quantum chemical investigations of their geometries and stabilities. J. Phys. Chem. B, 115, 1469-1484.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 1469-1484
-
-
Chawla, M.1
Sharma, P.2
Halder, S.3
Bhattacharyya, D.4
Mitra, A.5
-
12
-
-
34548353962
-
Mg2+binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs
-
Oliva, R., Tramontano, A. and Cavallo, L. (2007) Mg2+binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs. RNA, 13, 1427-1436.
-
(2007)
RNA
, vol.13
, pp. 1427-1436
-
-
Oliva, R.1
Tramontano, A.2
Cavallo, L.3
-
13
-
-
53249135077
-
Metal-ion-mediated base pairs in nucleic acids
-
Muller, J. (2008) Metal-ion-mediated base pairs in nucleic acids. Eur. J. Inorg. Chem., 3749-3763.
-
(2008)
Eur. J. Inorg. Chem.
, pp. 3749-3763
-
-
Muller, J.1
-
14
-
-
71549135214
-
Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs
-
Oliva, R. and Cavallo, L. (2009) Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs. J. Phys. Chem. B, 113, 15670-15678.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 15670-15678
-
-
Oliva, R.1
Cavallo, L.2
-
15
-
-
84873892798
-
Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: Molecular dynamics thermodynamics integration study
-
Krepl, M., Otyepka, M., Banas, P. and Sponer, J. (2013) Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study. J. Phys. Chem. B, 117, 1872-1879.
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 1872-1879
-
-
Krepl, M.1
Otyepka, M.2
Banas, P.3
Sponer, J.4
-
16
-
-
33644844986
-
Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions
-
Oliva, R., Cavallo, L. and Tramontano, A. (2006) Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions. Nucleic Acids Res., 34, 865-879.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 865-879
-
-
Oliva, R.1
Cavallo, L.2
Tramontano, A.3
-
17
-
-
81855169786
-
A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis
-
Reblova, K., Sponer, J.E., Spackova, N., Besseova, I. and Sponer, J. (2011) A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis. J. Phys. Chem. B, 115, 13897-13910.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 13897-13910
-
-
Reblova, K.1
Sponer, J.E.2
Spackova, N.3
Besseova, I.4
Sponer, J.5
-
18
-
-
34548291949
-
Leading RNA tertiary interactions: Structures energies, and water insertion of A-minor and P-interactions. A quantum chemical view
-
Sponer, J.E., Reblova, K., Mokdad, A., Sychrovsky, V., Leszczynski, J. and Sponer, J. (2007) Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view. J. Phys. Chem. B, 111, 9153-9164.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 9153-9164
-
-
Sponer, J.E.1
Reblova, K.2
Mokdad, A.3
Sychrovsky, V.4
Leszczynski, J.5
Sponer, J.6
-
19
-
-
84867761593
-
Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration
-
Besseova, I., Banas, P., Kuhrova, P., Kosinova, P., Otyepka, M. and Sponer, J. (2012) Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration. J. Phys. Chem. B, 116, 9899-9916.
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 9899-9916
-
-
Besseova, I.1
Banas, P.2
Kuhrova, P.3
Kosinova, P.4
Otyepka, M.5
Sponer, J.6
-
20
-
-
78650096290
-
Quantum chemical studies of nucleic acids: Can we construct a bridge to the RNA structural biology and bioinformatics communities?
-
Sponer, J., Sponer, J.E., Petrov, A.I. and Leontis, N.B. (2010) Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J. Phys. Chem. B, 114, 15723-15741.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 15723-15741
-
-
Sponer, J.1
Sponer, J.E.2
Petrov, A.I.3
Leontis, N.B.4
-
21
-
-
61949188840
-
Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations
-
Mladek, A., Sharma, P., Mitra, A., Bhattacharyya, D., Sponer, J. and Sponer, J.E. (2009) Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations. J. Phys. Chem. B, 113, 1743-1755.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 1743-1755
-
-
Mladek, A.1
Sharma, P.2
Mitra, A.3
Bhattacharyya, D.4
Sponer, J.5
Sponer, J.E.6
-
22
-
-
77951146318
-
On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies
-
Sharma, P., Chawla, M., Sharma, S. and Mitra, A. (2010) On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies. RNA, 16, 942-957.
-
(2010)
RNA
, vol.16
, pp. 942-957
-
-
Sharma, P.1
Chawla, M.2
Sharma, S.3
Mitra, A.4
-
23
-
-
77749316056
-
On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology
-
Sharma, P., Sponer, J.E., Sponer, J., Sharma, S., Bhattacharyya, D. and Mitra, A. (2010) On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology. J. Phys. Chem. B, 114, 3307-3320.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 3307-3320
-
-
Sharma, P.1
Sponer, J.E.2
Sponer, J.3
Sharma, S.4
Bhattacharyya, D.5
Mitra, A.6
-
24
-
-
79958208426
-
Contiguous metal-mediated base pairs comprising two Ag-I ions
-
Megger, D.A., Fonseca Guerra, C., Hoffmann, J., Brutschy, B., Bickelhaupt, F.M. and Muller, J. (2011) Contiguous metal-mediated base pairs comprising two Ag-I ions. Chem. Eur. J., 17, 6533-6544.
-
(2011)
Chem. Eur. J.
, vol.17
, pp. 6533-6544
-
-
Megger, D.A.1
Fonseca Guerra, C.2
Hoffmann, J.3
Brutschy, B.4
Bickelhaupt, F.M.5
Muller, J.6
-
25
-
-
33746049822
-
Performance of various density functionals for the hydrogen bonds in DNA base pairs
-
van der Wijst, T., Fonseca Guerra, C., Swart, M. and Bickelhaupt, F.M. (2006) Performance of various density functionals for the hydrogen bonds in DNA base pairs. Chem. Phys. Lett., 426, 415-421.
-
(2006)
Chem. Phys. Lett.
, vol.426
, pp. 415-421
-
-
Van Der Wijst, T.1
Fonseca Guerra, C.2
Swart, M.3
Bickelhaupt, F.M.4
-
26
-
-
11244321707
-
Hydrogen bonds of RNA are stronger than those of DNA but NMR monitors only presence of methyl substituent in Uracil/Thymine
-
Swart, M., Fonseca Guerra, C. and Bickelhaupt, F.M. (2004) Hydrogen bonds of RNA are stronger than those of DNA, but NMR monitors only presence of methyl substituent in Uracil/Thymine. J. Am. Chem. Soc., 126, 16718-16719.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 16718-16719
-
-
Swart, M.1
Fonseca Guerra, C.2
Bickelhaupt, F.M.3
-
27
-
-
0037124685
-
Orbital interactions in strong and weak hydrogen bonds are essential for DNA replication
-
Fonseca Guerra, C. and Bickelhaupt, F.M. (2002) Orbital interactions in strong and weak hydrogen bonds are essential for DNA replication. Angew. Chem. Int. Ed., 41, 2092-2095.
-
(2002)
Angew. Chem. Int. Ed.
, vol.41
, pp. 2092-2095
-
-
Fonseca Guerra, C.1
Bickelhaupt, F.M.2
-
28
-
-
0034600253
-
Hydrogen bonding in DNA base pairs: Reconciliation of theory and experiment
-
Fonseca Guerra, C., Bickelhaupt, F.M., Snijders, J.G. and Baerends, E.J. (2000) Hydrogen bonding in DNA base pairs: reconciliation of theory and experiment. J. Am. Chem. Soc., 122, 4117-4128.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 4117-4128
-
-
Fonseca Guerra, C.1
Bickelhaupt, F.M.2
Snijders, J.G.3
Baerends, E.J.4
-
29
-
-
0001063056
-
Reverse Watson-Crick Isocytosine-Cytosine and Guanine-Cytosine base pairs stabilized by the formation of the minor tautomers of bases. An ab Initio study in the gas phase and in a water cluster
-
Zhanpeisov, N.U., S poner, J. and Leszczynski, J. (1998) Reverse Watson-Crick Isocytosine-Cytosine and Guanine-Cytosine base pairs stabilized by the formation of the minor tautomers of bases. An ab Initio study in the gas phase and in a water cluster. J. Phys. Chem. A, 102, 10374-10379.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 10374-10379
-
-
Zhanpeisov, N.U.1
Sponer, J.2
Leszczynski, J.3
-
30
-
-
0036798116
-
RNA canonical and noncanonical base pairing types: A recognition method and complete repertoire
-
Lemieux, S. and Major, F. (2002) RNA canonical and noncanonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res., 30, 4250-4263.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4250-4263
-
-
Lemieux, S.1
Major, F.2
-
31
-
-
0022779159
-
Can the double helix be parallel?
-
Pattabiraman, N. (1986) Can the double helix be parallel? Biopolymers, 25, 1603-1606.
-
(1986)
Biopolymers
, vol.25
, pp. 1603-1606
-
-
Pattabiraman, N.1
-
32
-
-
0032564317
-
FTIR and UV spectroscopy of parallel-stranded DNAs with mixed A*T/G*C sequences and their A*T/I*C analogues
-
Mohammadi, S., Klement, R., Shchyolkina, A.K., Liquier, J., Jovin, T.M. and Taillandier, E. (1998) FTIR and UV spectroscopy of parallel-stranded DNAs with mixed A*T/G*C sequences and their A*T/I*C analogues. Biochemistry, 37, 16529-16537.
-
(1998)
Biochemistry
, vol.37
, pp. 16529-16537
-
-
Mohammadi, S.1
Klement, R.2
Shchyolkina, A.K.3
Liquier, J.4
Jovin, T.M.5
Taillandier, E.6
-
33
-
-
0025300695
-
A parallel stranded linear DNA duplex incorporating dG.dC base pairs
-
Rippe, K., Ramsing, N.B., Klement, R. and Jovin, T.M. (1990) A parallel stranded linear DNA duplex incorporating dG.dC base pairs. J. Biomol. Struct. Dyn., 7, 1199-1209.
-
(1990)
J. Biomol. Struct. Dyn.
, vol.7
, pp. 1199-1209
-
-
Rippe, K.1
Ramsing, N.B.2
Klement, R.3
Jovin, T.M.4
-
34
-
-
0001369096
-
Calorimetric characterization of parallel-stranded DNA: Stability conformational flexibility, and ion binding
-
Rentzeperis, D., Rippe, K., Jovin, T.M. and Marky, L.A. (1992) Calorimetric characterization of parallel-stranded DNA: stability, conformational flexibility, and ion binding. J. Am. Chem. Soc., 114, 5926-5928.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 5926-5928
-
-
Rentzeperis, D.1
Rippe, K.2
Jovin, T.M.3
Marky, L.A.4
-
35
-
-
84879103214
-
Structure of a class II preQ riboswitch reveals ligand recognition by a new fold
-
Liberman, J.A., Salim, M., Krucinska, J. and Wedekind, J.E. (2013) Structure of a class II preQ riboswitch reveals ligand recognition by a new fold. Nat. Chem. Biol., 9, 353-355.
-
(2013)
Nat. Chem. Biol.
, vol.9
, pp. 353-355
-
-
Liberman, J.A.1
Salim, M.2
Krucinska, J.3
Wedekind, J.E.4
-
36
-
-
0027191379
-
Structure of the archaeal transfer RNA nucleoside G*-15 (2-amino-4, 7-dihydro-4-oxo-7-beta-D-ribofuranosyl-1Hpyrrolo[ 2, 3-d]pyrimidine-5-carboximi dam ide (archaeosine)
-
Gregson, J.M., Crain, P.F., Edmonds, C.G., Gupta, R., Hashizume, T., Phillipson, D.W. and McCloskey, J.A. (1993) Structure of the archaeal transfer RNA nucleoside G*-15 (2-amino-4, 7-dihydro-4-oxo-7-beta-D-ribofuranosyl- 1Hpyrrolo[ 2, 3-d]pyrimidine-5-carboximi dam ide (archaeosine)). J. Biol. Chem., 268, 10076-10086.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 10076-10086
-
-
Gregson, J.M.1
Crain, P.F.2
Edmonds, C.G.3
Gupta, R.4
Hashizume, T.5
Phillipson, D.W.6
McCloskey, J.A.7
-
37
-
-
33846036096
-
The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
-
Berman, H., Henrick, K., Nakamura, H. and Markley, J.L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
Markley, J.L.4
-
38
-
-
0038690207
-
Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G basepairs
-
Sponer, J., Mokdad, A., Sponer, J.E., Spackova, N., Leszczynski, J. and Leontis, N.B. (2003) Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G basepairs. J. Mol. Biol., 330, 967-978.
-
(2003)
J. Mol. Biol.
, vol.330
, pp. 967-978
-
-
Sponer, J.1
Mokdad, A.2
Sponer, J.E.3
Spackova, N.4
Leszczynski, J.5
Leontis, N.B.6
-
39
-
-
84855712578
-
Understanding the sequence preference of recurrent RNA building blocks using quantum chemistry: The intrastrand RNA dinucleotide platform
-
Mladek, A., Sponer, J.E., Kulhanek, P., Lu, X.J., Olson, W.K. and Sponer, J. (2012) Understanding the sequence preference of recurrent RNA building blocks using quantum chemistry: the intrastrand RNA dinucleotide platform. J. Chem. Theory. Comput., 8, 335-347.
-
(2012)
J. Chem. Theory. Comput.
, vol.8
, pp. 335-347
-
-
Mladek, A.1
Sponer, J.E.2
Kulhanek, P.3
Lu, X.J.4
Olson, W.K.5
Sponer, J.6
-
40
-
-
26844533291
-
Sugar edge/sugar edge base pairs in RNA: Stabilities and structures from quantum chemical calculations
-
Sponer, J.E., Leszczynski, J., Sychrovsky, V. and Sponer, J. (2005) Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations. J. Phys. Chem. B, 109, 18680-18689.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 18680-18689
-
-
Sponer, J.E.1
Leszczynski, J.2
Sychrovsky, V.3
Sponer, J.4
-
41
-
-
77950226847
-
Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions
-
Morgado, C.A., Jurecka, P., Svozil, D., Hobza, P. and Sponer, J. (2010) Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Phys. Chem. Chem. Phys., 12, 3522-3534.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 3522-3534
-
-
Morgado, C.A.1
Jurecka, P.2
Svozil, D.3
Hobza, P.4
Sponer, J.5
-
42
-
-
20744441693
-
Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs
-
Sponer, J.E., Spackova, N., Leszczynski, J. and Sponer, J. (2005) Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs. J. Phys. Chem. B, 109, 11399-11410.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 11399-11410
-
-
Sponer, J.E.1
Spackova, N.2
Leszczynski, J.3
Sponer, J.4
-
43
-
-
21844446373
-
Aminoacylation and conformational properties of yeast mitochondrial tRNA mutants with respiratory deficiency
-
Francisci, S., De Luca, C., Oliva, R., Morea, V., Tramontano, A. and Frontali, L. (2005) Aminoacylation and conformational properties of yeast mitochondrial tRNA mutants with respiratory deficiency. RNA, 11, 914-927.
-
(2005)
RNA
, vol.11
, pp. 914-927
-
-
Francisci, S.1
De Luca, C.2
Oliva, R.3
Morea, V.4
Tramontano, A.5
Frontali, L.6
-
44
-
-
38649107661
-
Yeast as a model of human mitochondrial tRNA base substitutions: Investigation of the molecular basis of respiratory defects
-
Montanari, A., Besagni, C., De Luca, C., Morea, V., Oliva, R., Tramontano, A., Bolotin-Fukuhara, M., Frontali, L. and Francisci, S. (2008) Yeast as a model of human mitochondrial tRNA base substitutions: investigation of the molecular basis of respiratory defects. RNA, 14, 275-283.
-
(2008)
RNA
, vol.14
, pp. 275-283
-
-
Montanari, A.1
Besagni, C.2
De Luca, C.3
Morea, V.4
Oliva, R.5
Tramontano, A.6
Bolotin-Fukuhara, M.7
Frontali, L.8
Francisci, S.9
-
45
-
-
84857838609
-
Comprehensive survey and geometric classification of base triples in RNA structures
-
Abu Almakarem, A.S., Petrov, A.I., Stombaugh, J., Zirbel, C.L. and Leontis, N.B. (2012) Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Res., 40, 1407-1423.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 1407-1423
-
-
Abu Almakarem, A.S.1
Petrov, A.I.2
Stombaugh, J.3
Zirbel, C.L.4
Leontis, N.B.5
-
46
-
-
0043123152
-
Tools for the automatic identification and classification of RNA base pairs
-
Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H. and Westhof, E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3450-3460
-
-
Yang, H.1
Jossinet, F.2
Leontis, N.3
Chen, L.4
Westbrook, J.5
Berman, H.6
Westhof, E.7
-
47
-
-
0000189651
-
Density-functional thermochemistry. III. The role of exact exchange
-
Becke, A.D. (1993) Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys., 98, 5648-5652.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
48
-
-
11144255959
-
Density-functional thermochemistry. IV. A new dynamical correlation functional and implications for exactexchange mixing
-
Becke, A.D. (1996) Density-functional thermochemistry. IV. A new dynamical correlation functional and implications for exactexchange mixing. J. Chem. Phys., 104, 1040-1046.
-
(1996)
J. Chem. Phys.
, vol.104
, pp. 1040-1046
-
-
Becke, A.D.1
-
49
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
-
Lee, C., Yang, W. and Parr, R.G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B, 37, 785-789.
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
50
-
-
33746614482
-
Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen
-
Dunning, T.H. Jr (1989) Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys., 90, 1007-1023.
-
(1989)
J. Chem. Phys.
, vol.90
, pp. 1007-1023
-
-
Dunning Jr., T.H.1
-
51
-
-
84961985847
-
Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model
-
Barone, V. and Cossi, M. (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J. Phys. Chem. A, 102, 1995-2001.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 1995-2001
-
-
Barone, V.1
Cossi, M.2
-
52
-
-
84962349001
-
Energies structures, and electronic properties of molecules in solution with the C-PCM solvation model
-
Cossi, M., Rega, N., Scalmani, G. and Barone, V. (2003) Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J. Comp. Chem., 24, 669-681.
-
(2003)
J. Comp. Chem.
, vol.24
, pp. 669-681
-
-
Cossi, M.1
Rega, N.2
Scalmani, G.3
Barone, V.4
-
53
-
-
6944251055
-
Note on an approximation treatment for many-electron systems
-
M?ler, C. and Plesset, M.S. (1934) Note on an approximation treatment for many-electron systems. Phys. Rev., 46, 618-622.
-
(1934)
Phys. Rev.
, vol.46
, pp. 618-622
-
-
Mler, C.1
Plesset, M.S.2
-
54
-
-
84961980743
-
COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient
-
Klamt, A. and Schu?u?rmann, G. (1993) COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc. Perkin Trans. 2, 5, 799-805.
-
(1993)
J. Chem. Soc. Perkin Trans.
, vol.2
, pp. 799-805
-
-
Klamt, A.1
Schuurmann, G.2
-
55
-
-
84890021933
-
The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors
-
Boys, S.F. and Bernardi, F. (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys., 19, 553-566.
-
(1970)
Mol. Phys.
, vol.19
, pp. 553-566
-
-
Boys, S.F.1
Bernardi, F.2
-
56
-
-
0000965687
-
Structure, energetics, and dynamics of the nucleic Acid base pairs: Nonempirical ab initio calculations
-
Hobza, P. and S? poner, J. (1999) Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. Chem. Rev., 99, 3247-3276.
-
(1999)
Chem. Rev.
, vol.99
, pp. 3247-3276
-
-
Hobza, P.1
Sponer, J.2
-
57
-
-
0037010001
-
Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations
-
Hobza, P. and S? poner, J. (2002) Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations. J. Am. Chem. Soc., 124, 11802-11808.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 11802-11808
-
-
Hobza, P.1
Sponer, J.2
-
58
-
-
4043137165
-
Accurate interaction energies of hydrogen-bonded nucleic acid base pairs
-
S? poner, J., Jurecka, P. and Hobza, P. (2004) Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J. Am. Chem. Soc., 126, 10142-10151.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 10142-10151
-
-
Sponer, J.1
Jurecka, P.2
Hobza, P.3
-
59
-
-
0031274672
-
Interaction of DNA base pairs with various metal cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab Initio calculations on structures, energies, and nonadditivity of the interaction
-
Burda, J.V., S? poner, J., Leszczynski, J. and Hobza, P. (1997) Interaction of DNA base pairs with various metal cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab Initio calculations on structures, energies, and nonadditivity of the interaction. J. Phys. Chem. B, 101, 9670-9677.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 9670-9677
-
-
Burda, J.V.1
Sponer, J.2
Leszczynski, J.3
Hobza, P.4
-
60
-
-
0001063056
-
Reverse Watson-Crick Isocytosine-Cytosine and Guanine-Cytosine base pairs stabilized by the formation of the minor tautomers of bases. An ab initio study in the gas phase and in a water cluster
-
Zhanpeisov, N.U., S? poner, J. and Leszczynski, J. (1998) Reverse Watson-Crick Isocytosine-Cytosine and Guanine-Cytosine base pairs stabilized by the formation of the minor tautomers of bases. An ab initio study in the gas phase and in a water cluster. J. Phys. Chem. A, 102, 10374-10379.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 10374-10379
-
-
Zhanpeisov, N.U.1
Sponer, J.2
Leszczynski, J.3
-
61
-
-
17844383238
-
The B-to A-DNA transition and the reorganization of solvent at the DNA surface
-
Pastor, N. (2005) The B-to A-DNA transition and the reorganization of solvent at the DNA surface. Biophys. J., 88, 3262-3275.
-
(2005)
Biophys. J.
, vol.88
, pp. 3262-3275
-
-
Pastor, N.1
-
62
-
-
33646357500
-
RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics
-
Razga, F., Zacharias, M., Reblova, K., Koca, J. and Sponer, J. (2006) RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. Structure, 14, 825-835.
-
(2006)
Structure
, vol.14
, pp. 825-835
-
-
Razga, F.1
Zacharias, M.2
Reblova, K.3
Koca, J.4
Sponer, J.5
-
63
-
-
77950141432
-
An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods
-
Reblova, K., Strelcova, Z., Kulhanek, P., Besseova, I., Mathews, D.H., Nostrand, K.V., Yildirim, I., Turner, D.H. and Sponer, J. (2010) An RNA molecular switch: intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods. J. Chem. Theory. Comput., 2010, 910-929.
-
(2010)
J. Chem. Theory. Comput.
, vol.2010
, pp. 910-929
-
-
Reblova, K.1
Strelcova, Z.2
Kulhanek, P.3
Besseova, I.4
Mathews, D.H.5
Nostrand, K.V.6
Yildirim, I.7
Turner, D.H.8
Sponer, J.9
-
64
-
-
12844258405
-
Long-residency hydration cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex
-
Reblova, K., Spackova, N., Koca, J., Leontis, N.B. and Sponer, J. (2004) Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. Biophys. J., 87, 3397-3412.
-
(2004)
Biophys. J.
, vol.87
, pp. 3397-3412
-
-
Reblova, K.1
Spackova, N.2
Koca, J.3
Leontis, N.B.4
Sponer, J.5
-
65
-
-
15944404219
-
Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family
-
Sponer, J.E., Spackova, N., Kulhanek, P., Leszczynski, J. and Sponer, J. (2005) Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. J. Phys. Chem. A, 109, 2292-2301.
-
(2005)
J. Phys. Chem. A
, vol.109
, pp. 2292-2301
-
-
Sponer, J.E.1
Spackova, N.2
Kulhanek, P.3
Leszczynski, J.4
Sponer, J.5
|