-
1
-
-
84909580167
-
The expanding view of RNA and DNA function
-
Breaker, R. R. and Joyce, G. F. (2014) The expanding view of RNA and DNA function. Chem. Biol., 21, 1059-1065.
-
(2014)
Chem. Biol.
, vol.21
, pp. 1059-1065
-
-
Breaker, R.R.1
Joyce, G.F.2
-
2
-
-
84902192900
-
Hierarchy of RNA functional dynamics
-
Mustoe, A. M., Brooks, C. L. and Al-Hashimi, H. M. (2014) Hierarchy of RNA functional dynamics. Annu. Rev. Biochem., 83, 441-466.
-
(2014)
Annu. Rev. Biochem.
, vol.83
, pp. 441-466
-
-
Mustoe, A.M.1
Brooks, C.L.2
Al-Hashimi, H.M.3
-
3
-
-
84858694575
-
RNA unwinding from reweighted pulling simulations
-
Colizzi, F. and Bussi, G. (2012) RNA unwinding from reweighted pulling simulations. J. Am. Chem. Soc., 134, 5173-5179.
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 5173-5179
-
-
Colizzi, F.1
Bussi, G.2
-
4
-
-
84885818229
-
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
-
Chen, A. A. and Garc, A. E. (2013) High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations. Proc. Natl. Acad. Sci. U. S. A., 110, 16820-16825.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 16820-16825
-
-
Chen, A.A.1
Garc, A.E.2
-
5
-
-
84875989318
-
Computer folding of RNA tetraloops are we there yet
-
Khrova, P., Bans, P., Best, R. B., Sponer, J. and Otyepka, M. (2013) Computer folding of RNA tetraloops are we there yet J. Chem. Theory Comput., 9, 2115-2125.
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2115-2125
-
-
Khrova, P.1
Bans, P.2
Best, R.B.3
Sponer, J.4
Otyepka, M.5
-
6
-
-
84874881081
-
A dynamic structural model of expanded RNA CAG repeats: A refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations
-
Yildirim, I., Park, H., Disney, M. D. and Schatz, G. C. (2013) A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations. J. Am. Chem. Soc., 135, 3528-3538.
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 3528-3538
-
-
Yildirim, I.1
Park, H.2
Disney, M.D.3
Schatz, G.C.4
-
7
-
-
84908658478
-
Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA
-
Musiani, F., Rossetti, G., Capece, L., Gerger, T. M., Micheletti, C., Varani, G. and Carloni, P. (2014) Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA. J. Am. Chem. Soc., 136, 15631-15637.
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 15631-15637
-
-
Musiani, F.1
Rossetti, G.2
Capece, L.3
Gerger, T.M.4
Micheletti, C.5
Varani, G.6
Carloni, P.7
-
8
-
-
84927656679
-
Ion distributions around left-and right-handed DNA and RNA duplexes: A comparative study
-
Pan, F., Roland, C. and Sagui, C. (2014) Ion distributions around left-and right-handed DNA and RNA duplexes: a comparative study. Nucleic Acids Res., 42, 13981-13996.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 13981-13996
-
-
Pan, F.1
Roland, C.2
Sagui, C.3
-
9
-
-
84901047861
-
Molecular dynamics simulations of nucleic acids. from tetranucleotides to the ribosome
-
Sponer, J., Bans, P., Jurecka, P., Zgarbov, M., Khrov, P., Havrila, M., Krepl, M., Stadlbauer, P. and Otyepka, M. (2014) Molecular dynamics simulations of nucleic acids. from tetranucleotides to the ribosome. J. Phys. Chem. Lett., 5, 1771-1782.
-
(2014)
J. Phys. Chem. Lett.
, vol.5
, pp. 1771-1782
-
-
Sponer, J.1
Bans, P.2
Jurecka, P.3
Zgarbov, M.4
Khrov, P.5
Havrila, M.6
Krepl, M.7
Stadlbauer, P.8
Otyepka, M.9
-
11
-
-
44149101971
-
Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
-
Ding, F., Sharma, S., Chalasani, P., Demidov, V. V., Broude, N. E. and Dokholyan, N. V. (2008) Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA, 14, 1164-1173.
-
(2008)
RNA
, vol.14
, pp. 1164-1173
-
-
Ding, F.1
Sharma, S.2
Chalasani, P.3
Demidov, V.V.4
Broude, N.E.5
Dokholyan, N.V.6
-
12
-
-
58249111738
-
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
-
Jonikas, M. A., Radmer, R. J., Laederach, A., Das, R., Pearlman, S., Herschlag, D. and Altman, R. B. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA, 15, 189-199.
-
(2009)
RNA
, vol.15
, pp. 189-199
-
-
Jonikas, M.A.1
Radmer, R.J.2
Laederach, A.3
Das, R.4
Pearlman, S.5
Herschlag, D.6
Altman, R.B.7
-
13
-
-
79953795893
-
Physics-based de novo prediction of RNA 3D structures
-
Cao, S. and Chen, S.-J. (2011) Physics-based de novo prediction of RNA 3D structures. J. Phys. Chem. B, 115, 4216-4226.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 4216-4226
-
-
Cao, S.1
Chen, S.-J.2
-
14
-
-
84877022321
-
Coarse-grained model for predicting RNA folding thermodynamics
-
Denesyuk, N. A. and Thirumalai, D. (2013) Coarse-grained model for predicting RNA folding thermodynamics. J. Phys. Chem. B, 117, 4901-4911.
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 4901-4911
-
-
Denesyuk, N.A.1
Thirumalai, D.2
-
15
-
-
84875471554
-
RNA 3D structure prediction by using a coarse-grained model and experimental data
-
Xia, Z., Bell, D. R., Shi, Y. and Ren, P. (2013) RNA 3D structure prediction by using a coarse-grained model and experimental data. J. Phys. Chem. B, 117, 3135-3144.
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 3135-3144
-
-
Xia, Z.1
Bell, D.R.2
Shi, Y.3
Ren, P.4
-
16
-
-
84880152678
-
Coarse-grained simulations of RNA and DNA duplexes
-
Cragnolini, T., Derreumaux, P. and Pasquali, S. (2013) Coarse-grained simulations of RNA and DNA duplexes. J. Phys. Chem. B, 117, 8047-8060.
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 8047-8060
-
-
Cragnolini, T.1
Derreumaux, P.2
Pasquali, S.3
-
17
-
-
84903139508
-
A nucleotide-level coarse-grained model of RNA
-
Sulc, P., Romano, F., Ouldridge, T. E., Doye, J. P. and Louis, A. A. (2014) A nucleotide-level coarse-grained model of RNA. J. Chem. Phys., 140, 235102.
-
(2014)
J. Chem. Phys.
, vol.140
, pp. 235102
-
-
Sulc, P.1
Romano, F.2
Ouldridge, T.E.3
Doye, J.P.4
Louis, A.A.5
-
18
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter atomic analysis
-
Tirion, M. M. (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett., 77, 1905-1908.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
19
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen, K. (1998) Analysis of domain motions by approximate normal mode calculations. Proteins, 33, 417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
20
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar, I., Atilgan, A. R. and Erman, B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des., 2, 173-181.
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
21
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, O. and Bahar, I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J., 80, 505-515.
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
22
-
-
2442543557
-
Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models
-
Micheletti, C., Carloni, P. and Maritan, A. (2004) Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models. Proteins, 55, 635-645.
-
(2004)
Proteins
, vol.55
, pp. 635-645
-
-
Micheletti, C.1
Carloni, P.2
Maritan, A.3
-
23
-
-
84876346374
-
Comparing proteins by their internal dynamics: Exploring structure-function relationships beyond static structural alignments
-
Micheletti, C. (2013) Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Phys. Life Rev., 10, 1-26.
-
(2013)
Phys. Life Rev.
, vol.10
, pp. 1-26
-
-
Micheletti, C.1
-
24
-
-
0036077875
-
Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
-
Delarue, M. and Sanejouand, Y.-H. (2002) Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J. Mol. Biol., 320, 1011-1024.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 1011-1024
-
-
Delarue, M.1
Sanejouand, Y.-H.2
-
25
-
-
84890463144
-
Evaluation of protein elastic network models based on an analysis of collective motions
-
Fuglebakk, E., Reuter, N. and Hinsen, K. (2013) Evaluation of protein elastic network models based on an analysis of collective motions. J. Chem. Theory Comput., 9, 5618-5628.
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 5618-5628
-
-
Fuglebakk, E.1
Reuter, N.2
Hinsen, K.3
-
26
-
-
0032483483
-
Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms
-
Bahar, I. and Jernigan, R. L. (1998) Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. J. Mol. Biol., 281, 871-884.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 871-884
-
-
Bahar, I.1
Jernigan, R.L.2
-
27
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama, F., Valle, M., Frank, J. and Brooks, C. L. (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. U. S. A., 100, 9319-9323.
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks, C.L.4
-
28
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
Wang, Y., Rader, A., Bahar, I. and Jernigan, R. L. (2004) Global ribosome motions revealed with elastic network model. J. Struct. Biol., 147, 302-314.
-
(2004)
J. Struct. Biol.
, vol.147
, pp. 302-314
-
-
Wang, Y.1
Rader, A.2
Bahar, I.3
Jernigan, R.L.4
-
29
-
-
25844441847
-
Comparison of mode analyses at different resolutions applied to nucleic acid systems
-
Van Wynsberghe, A. W. and Cui, Q. (2005) Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys. J., 89, 2939-2949.
-
(2005)
Biophys. J.
, vol.89
, pp. 2939-2949
-
-
Van Wynsberghe, A.W.1
Cui, Q.2
-
30
-
-
27744512500
-
Comparison of tRNA motions in the free and ribosomal bound structures
-
Wang, Y. and Jernigan, R. L. (2005) Comparison of tRNA motions in the free and ribosomal bound structures. Biophys. J., 89, 3399-3409.
-
(2005)
Biophys. J.
, vol.89
, pp. 3399-3409
-
-
Wang, Y.1
Jernigan, R.L.2
-
31
-
-
44849090619
-
Analyzing the flexibility of RNA structures by constraint counting
-
Fulle, S. and Gohlke, H. (2008) Analyzing the flexibility of RNA structures by constraint counting. Biophys. J., 94, 4202-4219.
-
(2008)
Biophys. J.
, vol.94
, pp. 4202-4219
-
-
Fulle, S.1
Gohlke, H.2
-
32
-
-
66149167201
-
Collective dynamics of the ribosomal tunnel revealed by elastic network modeling
-
Kurkcuoglu, O., Kurkcuoglu, Z., Doruker, P. and Jernigan, R. L. (2009) Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins, 75, 837-845.
-
(2009)
Proteins
, vol.75
, pp. 837-845
-
-
Kurkcuoglu, O.1
Kurkcuoglu, Z.2
Doruker, P.3
Jernigan, R.L.4
-
33
-
-
84901471787
-
Elastic network models capture the motions apparent within ensembles of RNA structures
-
Zimmermann, M. T. and Jernigan, R. L. (2014) Elastic network models capture the motions apparent within ensembles of RNA structures. RNA, 20, 792-804.
-
(2014)
RNA
, vol.20
, pp. 792-804
-
-
Zimmermann, M.T.1
Jernigan, R.L.2
-
34
-
-
84890534523
-
Elastic network models of nucleic acids flexibility
-
Setny, P. and Zacharias, M. (2013) Elastic network models of nucleic acids flexibility. J. Chem. Theory Comput., 9, 5460-5470.
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 5460-5470
-
-
Setny, P.1
Zacharias, M.2
-
35
-
-
33747829284
-
OGNM: Online computation of structural dynamics using the Gaussian network model
-
Yang, L.-W., Rader, A., Liu, X., Jursa, C. J., Chen, S. C., Karimi, H. A. and Bahar, I. (2006) oGNM: online computation of structural dynamics using the Gaussian network model. Nucleic Acids Res., 34, W24-W31.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W24-W31
-
-
Yang, L.-W.1
Rader, A.2
Liu, X.3
Jursa, C.J.4
Chen, S.C.5
Karimi, H.A.6
Bahar, I.7
-
36
-
-
16244412610
-
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (shape)
-
Merino, E. J., Wilkinson, K. A., Coughlan, J. L. and Weeks, K. M. (2005) RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (shape). J. Am. Chem. Soc., 127, 4223-4231.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 4223-4231
-
-
Merino, E.J.1
Wilkinson, K.A.2
Coughlan, J.L.3
Weeks, K.M.4
-
37
-
-
79960611669
-
Exploring RNA structural codes with SHAPE chemistry
-
Weeks, K. M. and Mauger, D. M. (2011) Exploring RNA structural codes with SHAPE chemistry. Acc. Chem. Res., 44, 1280-1291.
-
(2011)
Acc. Chem. Res.
, vol.44
, pp. 1280-1291
-
-
Weeks, K.M.1
Mauger, D.M.2
-
38
-
-
84859942952
-
The mechanisms of RNA SHAPE chemistry
-
McGinnis, J. L., Dunkle, J. A., Cate, J. H. and Weeks, K. M. (2012) The mechanisms of RNA SHAPE chemistry. J. Am. Chem. Soc., 134, 6617-6624.
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 6617-6624
-
-
McGinnis, J.L.1
Dunkle, J.A.2
Cate, J.H.3
Weeks, K.M.4
-
39
-
-
84923574631
-
Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT
-
Kirmizialtin, S., Hennelly, S. P., Schug, A., Onuchic, J. N. and Sanbonmatsu, K. Y. (2015) Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods Enzymol., 553, 215-234.
-
(2015)
Methods Enzymol.
, vol.553
, pp. 215-234
-
-
Kirmizialtin, S.1
Hennelly, S.P.2
Schug, A.3
Onuchic, J.N.4
Sanbonmatsu, K.Y.5
-
40
-
-
0034254780
-
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for GU pairs: One hydrogen bond for each GU pair in r(GGCGUGCC)2 and two for each GU pair in r(GAGUGCUC) 2
-
Chen, X., McDowell, J. A., Kierzek, R., Krugh, T. R. and Turner, D. H. (2000) Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for GU pairs: one hydrogen bond for each GU pair in r(GGCGUGCC)2 and two for each GU pair in r(GAGUGCUC)2. Biochemistry, 39, 8970-8982.
-
(2000)
Biochemistry
, vol.39
, pp. 8970-8982
-
-
Chen, X.1
McDowell, J.A.2
Kierzek, R.3
Krugh, T.R.4
Turner, D.H.5
-
41
-
-
0345531092
-
The common and the distinctive features of the bulged-G motif based on a 1. 04 a resolution RNA structure
-
Correll, C. C., Beneken, J., Plantinga, M. J., Lubbers, M. and Chan, Y.-L. (2003) The common and the distinctive features of the bulged-G motif based on a 1. 04 a resolution RNA structure. Nucleic Acids Res., 31, 6806-6818.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6806-6818
-
-
Correll, C.C.1
Beneken, J.2
Plantinga, M.J.3
Lubbers, M.4
Chan, Y.-L.5
-
42
-
-
0030476765
-
Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
-
Scott, W. G., Murray, J. B., Arnold, J. R., Stoddard, B. L. and Klug, A. (1996) Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science, 274, 2065-2069.
-
(1996)
Science
, vol.274
, pp. 2065-2069
-
-
Scott, W.G.1
Murray, J.B.2
Arnold, J.R.3
Stoddard, B.L.4
Klug, A.5
-
43
-
-
10644250950
-
Structural basis for discriminative regulation of gene expression by adenine-and guanine-sensing mRNAs
-
Serganov, A., Yuan, Y.-R., Pikovskaya, O., Polonskaia, A., Malinina, L., Phan, A. T., Hobartner, C., Micura, R., Breaker, R. R. and Patel, D. J. (2004) Structural basis for discriminative regulation of gene expression by adenine-and guanine-sensing mRNAs. Chem. Biol., 11, 1729-1741.
-
(2004)
Chem. Biol.
, vol.11
, pp. 1729-1741
-
-
Serganov, A.1
Yuan, Y.-R.2
Pikovskaya, O.3
Polonskaia, A.4
Malinina, L.5
Phan, A.T.6
Hobartner, C.7
Micura, R.8
Breaker, R.R.9
Patel, D.J.10
-
44
-
-
32644451166
-
Molecular dynamics simulations of sarcin-ricin rRNA motif
-
Spackov, N. and Sponer, J. (2006) Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Res., 34, 697-708.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 697-708
-
-
Spackov, N.1
Sponer, J.2
-
45
-
-
77649274141
-
Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch
-
Priyakumar, U. D. and MacKerell, A. D. (2010) Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. J. Mol. Biol., 396, 1422-1438.
-
(2010)
J. Mol. Biol.
, vol.396
, pp. 1422-1438
-
-
Priyakumar, U.D.1
MacKerell, A.D.2
-
46
-
-
80052240487
-
Role of ligand binding in structural organization of add A-riboswitch aptamer: A molecular dynamics simulation
-
Gong, Z., Zhao, Y., Chen, C. and Xiao, Y. (2011) Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation. J. Biomol. Struct. Dyn., 29, 403-416.
-
(2011)
J. Biomol. Struct. Dyn.
, vol.29
, pp. 403-416
-
-
Gong, Z.1
Zhao, Y.2
Chen, C.3
Xiao, Y.4
-
47
-
-
84879283831
-
Loop-loop interaction in an adenine-sensing riboswitch: A molecular dynamics study
-
Allnr, O., Nilsson, L. and Villa, A. (2013) Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study. RNA, 19, 916-926.
-
(2013)
RNA
, vol.19
, pp. 916-926
-
-
Allnr, O.1
Nilsson, L.2
Villa, A.3
-
48
-
-
84885985615
-
Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
-
Di Palma, F., Colizzi, F. and Bussi, G. (2013) Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch. RNA, 19, 1517-1524.
-
(2013)
RNA
, vol.19
, pp. 1517-1524
-
-
Di Palma, F.1
Colizzi, F.2
Bussi, G.3
-
49
-
-
84964697420
-
Kissing loop interaction in adenine riboswitch: Insights from umbrella sampling simulations
-
Di Palma, F., Bottaro, S. and Bussi, G. (2015) Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. BMC Bioinform., 16(Suppl. 9), S6.
-
(2015)
BMC Bioinform
, vol.16
, pp. S6
-
-
Di Palma, F.1
Bottaro, S.2
Bussi, G.3
-
50
-
-
84875592758
-
GROMACS 4. 5: A high-throughput and highly parallel open source molecular simulation toolkit
-
Pronk, S., Pll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van derSpoel, D. et al. (2013) GROMACS 4. 5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29, 845-854.
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Pll, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
Apostolov, R.6
Shirts, M.R.7
Smith, J.C.8
Kasson, P.M.9
Van Der Spoel, D.10
-
51
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and Simmerling, C. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins, 65, 712-725.
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
52
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of conformers
-
Prez, A., Marchn, I., Svozil, D., Sponer, J., Cheatham, T. E. III, Laughton, C. A. and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of-conformers. Biophys. J., 92, 3817-3829.
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Prez, A.1
Marchn, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
53
-
-
78651294111
-
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
-
Bans, P., Hollas, D., Zgarbov, M., Jurecka, P., Orozco, M., Cheatham, T. E. III, Sponer, J. and Otyepka, M. (2010) Performance of molecular mechanics force fields for RNA simulations: stability of UUCG and GNRA hairpins. J. Chem. Theory Comput., 6, 3836-3849.
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3836-3849
-
-
Bans, P.1
Hollas, D.2
Zgarbov, M.3
Jurecka, P.4
Orozco, M.5
Cheatham, T.E.6
Sponer, J.7
Otyepka, M.8
-
54
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
Bussi, G., Donadio, D. and Parrinello, M. (2007) Canonical sampling through velocity rescaling. J. Chem. Phys., 126, 014101.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
55
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J., Postma, J. P. M., vanGunsteren, W. F., DiNola, A. and Haak, J. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.5
-
56
-
-
33846823909
-
Particle mesh Ewald: An N log (N) method for Ewald sums in large systems
-
Darden, T., York, D. and Pedersen, L. (1993) Particle mesh Ewald: an N log (N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
57
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
Hess, B., Bekker, H., Berendsen, H. J. and Fraaije, J. G. (1997) LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem., 18, 1463-1472.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.3
Fraaije, J.G.4
-
58
-
-
0344796204
-
Ion-water interaction potentials derived from free energy perturbation simulations
-
Aaqvist, J. (1990) Ion-water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem., 94, 8021-8024.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8021-8024
-
-
Aaqvist, J.1
-
59
-
-
0029636784
-
Mechanism and thermodynamics of ion selectivity in aqueous solutions of 18-crown-6 ether: A molecular dynamics study
-
Dang, L. X. (1995) Mechanism and thermodynamics of ion selectivity in aqueous solutions of 18-crown-6 ether: a molecular dynamics study. J. Am. Chem. Soc., 117, 6954-6960.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 6954-6960
-
-
Dang, L.X.1
-
60
-
-
2942532422
-
Development and testing of a general AMBER force field
-
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. and Case, D. A. (2004) Development and testing of a general AMBER force field. J. Comput. Chem., 25, 1157-1174.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
61
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch, W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Cryst., 32, 922-923.
-
(1976)
Acta Cryst.
, vol.32
, pp. 922-923
-
-
Kabsch, W.1
-
62
-
-
28844456158
-
Allostery in a coarse-grained model of protein dynamics
-
Ming, D. and Wall, M. (2005) Allostery in a coarse-grained model of protein dynamics. Phys. Rev. Lett., 95, 198103.
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 198103
-
-
Ming, D.1
Wall, M.2
-
63
-
-
43049104657
-
Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families
-
Zen, A., Carnevale, V., Lesk, A. M. and Micheletti, C. (2008) Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. Protein Sci., 17, 918-929.
-
(2008)
Protein Sci.
, vol.17
, pp. 918-929
-
-
Zen, A.1
Carnevale, V.2
Lesk, A.M.3
Micheletti, C.4
-
64
-
-
23244442698
-
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: Myosin versus kinesin
-
Zheng, W. and Brooks, B. R. (2005) Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophys. J., 89, 167-178.
-
(2005)
Biophys. J.
, vol.89
, pp. 167-178
-
-
Zheng, W.1
Brooks, B.R.2
-
65
-
-
0037022347
-
Flexibility and packing in proteins
-
Halle, B. (2002) Flexibility and packing in proteins. Proc. Natl. Acad. Sci. U. S. A., 99, 1274-1279.
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, pp. 1274-1279
-
-
Halle, B.1
-
66
-
-
34547702378
-
Structural and dynamical alignment of enzymes with partial structural similarity
-
Carnevale, V., Pontiggia, F. and Micheletti, C. (2007) Structural and dynamical alignment of enzymes with partial structural similarity. J. Phys. : Condens. Matter, 19, 285206.
-
(2007)
J. Phys. : Condens. Matter
, vol.19
, pp. 285206
-
-
Carnevale, V.1
Pontiggia, F.2
Micheletti, C.3
-
67
-
-
84901436960
-
RNA secondary structure modeling at consistent high accuracy using differential SHAPE
-
Rice, G. M., Leonard, C. W. and Weeks, K M. (2014) RNA secondary structure modeling at consistent high accuracy using differential SHAPE. RNA, 20, 846-854.
-
(2014)
RNA
, vol.20
, pp. 846-854
-
-
Rice, G.M.1
Leonard, C.W.2
Weeks, K.M.3
-
68
-
-
84888642158
-
PLUMED 2: New feathers for an old bird
-
Tribello, G. A., Bonomi, M., Branduardi, D., Camilloni, C. and Bussi, G. (2014) PLUMED 2: new feathers for an old bird. Comput. Phys. Commun., 185, 604-613.
-
(2014)
Comput. Phys. Commun.
, vol.185
, pp. 604-613
-
-
Tribello, G.A.1
Bonomi, M.2
Branduardi, D.3
Camilloni, C.4
Bussi, G.5
-
69
-
-
33745635350
-
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
-
Serganov, A., Polonskaia, A., Phan, A. T., Breaker, R. R. and Patel, D. J. (2006) Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature, 441, 1167-1171.
-
(2006)
Nature
, vol.441
, pp. 1167-1171
-
-
Serganov, A.1
Polonskaia, A.2
Phan, A.T.3
Breaker, R.R.4
Patel, D.J.5
-
70
-
-
84906260782
-
Base pair fraying in molecular dynamics simulations of DNA and RNA
-
Zgarbov, M., Otyepka, M., Sponer, J., Lankas, F. and Jurecka, P. (2014) Base pair fraying in molecular dynamics simulations of DNA and RNA. J. Chem. Theory Comput., 10, 3177-3189.
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 3177-3189
-
-
Zgarbov, M.1
Otyepka, M.2
Sponer, J.3
Lankas, F.4
Jurecka, P.5
-
71
-
-
84964693274
-
Ionic strength independence of charge distributions in solvation of biomolecules
-
Virtanen, J. J., Sosnick, T. R. and Freed, K. F. (2014) Ionic strength independence of charge distributions in solvation of biomolecules. J. Chem. Phys., 141, 22D503.
-
(2014)
J. Chem. Phys.
, vol.141
, pp. 22D503
-
-
Virtanen, J.J.1
Sosnick, T.R.2
Freed, K.F.3
-
72
-
-
35948966376
-
Spontaneous formation of KCl aggregates in biomolecular simulations: A force field issue
-
Auffinger, P., Cheatham, T. E. and Vaiana, A. C. (2007) Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue J. Chem. Theory Comput., 3, 1851-1859.
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1851-1859
-
-
Auffinger, P.1
Cheatham, T.E.2
Vaiana, A.C.3
-
73
-
-
49449085241
-
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
-
Joung, I. S. and Cheatham, T. E. III (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B, 112, 9020-9041.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
74
-
-
0032831634
-
Relationship between internucleotide linkage geometry and the stability of RNA
-
Soukup, G. A. and Breaker, R. R. (1999) Relationship between internucleotide linkage geometry and the stability of RNA. RNA, 5, 1308-1325.
-
(1999)
RNA
, vol.5
, pp. 1308-1325
-
-
Soukup, G.A.1
Breaker, R.R.2
-
75
-
-
0015511563
-
Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation
-
Altona, C. T. and Sundaralingam, M. (1972) Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation. J. Am. Chem. Soc., 94, 8205-8212.
-
(1972)
J. Am. Chem. Soc.
, vol.94
, pp. 8205-8212
-
-
Altona, C.T.1
Sundaralingam, M.2
-
76
-
-
0015913888
-
Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants
-
Altona, C. T. and Sundaralingam, M. (1973) Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants. J. Am. Chem. Soc., 95, 2333-3344.
-
(1973)
J. Am. Chem. Soc.
, vol.95
, pp. 2333-3344
-
-
Altona, C.T.1
Sundaralingam, M.2
-
77
-
-
84875865461
-
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
-
Hajdin, C. E., Bellaousov, S., Huggins, W., Leonard, C. W., Mathews, D. H. and Weeks, K. M. (2013) Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc. Natl. Acad. Sci. U. S. A., 110, 5498-5503.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 5498-5503
-
-
Hajdin, C.E.1
Bellaousov, S.2
Huggins, W.3
Leonard, C.W.4
Mathews, D.H.5
Weeks, K.M.6
-
78
-
-
0035906639
-
Quantitative analysis of nucleic acid three-dimensional structures
-
Gendron, P., Lemieux, S. and Major, F. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308, 919-936.
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 919-936
-
-
Gendron, P.1
Lemieux, S.2
Major, F.3
-
79
-
-
84941094198
-
The role of nucleobase interactions in RNA structure and dynamics
-
Bottaro, S., Di Palma, F. and Bussi, G. (2014) The role of nucleobase interactions in RNA structure and dynamics. Nucleic Acids Res., 42, 13306-13314.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 13306-13314
-
-
Bottaro, S.1
Di Palma, F.2
Bussi, G.3
-
81
-
-
77957958670
-
Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT
-
Fiorucci, S. and Zacharias, M. (2010) Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT. Proteins, 78, 3131-3139.
-
(2010)
Proteins
, vol.78
, pp. 3131-3139
-
-
Fiorucci, S.1
Zacharias, M.2
|