-
1
-
-
3142657230
-
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
-
Kalodimos, C.G., Biris, N., Bonvin, A.M., Levandoski, M.M., Guennuegues, M., Boelens, R. and Kaptein, R. (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science, 305, 386-389.
-
(2004)
Science
, vol.305
, pp. 386-389
-
-
Kalodimos, C.G.1
Biris, N.2
Bonvin, A.M.3
Levandoski, M.M.4
Guennuegues, M.5
Boelens, R.6
Kaptein, R.7
-
2
-
-
4344581629
-
Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the lac repressor system
-
Kalodimos, C.G., Boelens, R. and Kaptein, R. (2004) Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the Lac repressor system. Chem. Rev., 104, 3567-3586.
-
(2004)
Chem. Rev
, vol.104
, pp. 3567-3586
-
-
Kalodimos, C.G.1
Boelens, R.2
Kaptein, R.3
-
3
-
-
33750078971
-
NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA
-
Iwahara, J., Zweckstetter, M. and Clore, G.M. (2006) NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA. Proc. Natl. Acad. Sci. U.S.A., 103, 10562-10567.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 10562-10567
-
-
Iwahara, J.1
Zweckstetter, M.2
Clore, G.M.3
-
4
-
-
31544448614
-
Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy
-
Iwahara, J. and Clore, G.M. (2006) Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy. J. Am. Chem. Soc., 128, 404-405.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 404-405
-
-
Iwahara, J.1
Clore, G.M.2
-
5
-
-
35548943472
-
Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement
-
Clore, G.M., Tang, C. and Iwahara, J. (2007) Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr. Opin. Struct. Biol., 17, 603-616.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 603-616
-
-
Clore, G.M.1
Tang, C.2
Iwahara, J.3
-
6
-
-
72149127671
-
How a protein searches for its site on DNA: The mechanism of facilitated diffusion
-
Mirny, L., Slutsky, M., Wunderlich, Z., Tafvizi, A., Leith, J. and Kosmrlj, A. (2009) How a protein searches for its site on DNA: The mechanism of facilitated diffusion. J. Phys. A Math. Theor., 42, 434013.
-
(2009)
J. Phys. A Math. Theor
, vol.42
, pp. 434013
-
-
Mirny, L.1
Slutsky, M.2
Wunderlich, Z.3
Tafvizi, A.4
Leith, J.5
Kosmrlj, A.6
-
7
-
-
77949397232
-
Facilitated search of proteins on DNA: Correlations are important
-
Das, R.K. and Kolomeisky, A.B. (2010) Facilitated search of proteins on DNA: correlations are important. Phys. Chem. Chem. Phys., 12, 2999-3004.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 2999-3004
-
-
Das, R.K.1
Kolomeisky, A.B.2
-
8
-
-
80052437901
-
Theoretical and computational modeling of target-site search kinetics in vitro and in vivo
-
Koslover, E.F., Díaz de la Rosa, M.A. and Spakowitz, A.J. (2011) Theoretical and computational modeling of target-site search kinetics in vitro and in vivo. Biophys. J., 101, 856-865.
-
(2011)
Biophys. J.
, vol.101
, pp. 856-865
-
-
Koslover, E.F.1
De Díaz La Rosa, M.A.2
Spakowitz, A.J.3
-
9
-
-
79251584676
-
Physics of protein-DNA interactions: Mechanisms of facilitated target search
-
Kolomeisky, A.B. (2011) Physics of protein-DNA interactions: Mechanisms of facilitated target search. Phys. Chem. Chem. Phys., 13, 2088-2095.
-
(2011)
Phys. Chem. Chem. Phys
, vol.13
, pp. 2088-2095
-
-
Kolomeisky, A.B.1
-
10
-
-
77649111696
-
Insights into the sliding movement of the LAC repressor nonspecifically bound to DNA
-
Furini, S., Domene, C. and Cavalcanti, S. (2010) Insights into the sliding movement of the lac repressor nonspecifically bound to DNA. J. Phys. Chem. B, 114, 2238-2245.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 2238-2245
-
-
Furini, S.1
Domene, C.2
Cavalcanti, S.3
-
11
-
-
77952316521
-
Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains
-
Temiz, A.N., Benos, P.V. and Camacho, C.J. (2010) Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains. Nucleic Acids Res., 38, 2134-2144.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 2134-2144
-
-
Temiz, A.N.1
Benos, P.V.2
Camacho, C.J.3
-
12
-
-
79960017777
-
Protein-DNA recognition triggered by a DNA conformational switch
-
Bouvier, B., Zakrzewska, K. and Lavery, R. (2011) Protein-DNA recognition triggered by a DNA conformational switch. Angew. Chem. Int. Ed. Engl., 50, 6516-6518.
-
(2011)
Angew. Chem. Int. Ed. Engl
, vol.50
, pp. 6516-6518
-
-
Bouvier, B.1
Zakrzewska, K.2
Lavery, R.3
-
13
-
-
80052467650
-
The binding process of a nonspecific enzyme with DNA
-
Chen, C. and Pettitt, B.M. (2011) The binding process of a nonspecific enzyme with DNA. Biophys. J., 101, 1139-1147.
-
(2011)
Biophys. J.
, vol.101
, pp. 1139-1147
-
-
Chen, C.1
Pettitt, B.M.2
-
14
-
-
84876554311
-
DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence
-
Furini, S., Barbini, P. and Domene, C. (2013) DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence. Nucleic Acids Res., 41, 3963-3972.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 3963-3972
-
-
Furini, S.1
Barbini, P.2
Domene, C.3
-
15
-
-
84919628747
-
Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models
-
Ando, T. and Skolnick, J. (2014) Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models. Plos comput. Biol., 10, e1003990.
-
(2014)
Plos Comput. Biol
, vol.10
, pp. e1003990
-
-
Ando, T.1
Skolnick, J.2
-
16
-
-
80051862247
-
DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity
-
Sela, I. and Lukatsky, D. (2011) DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity. Biophys. J., 101, 160-166.
-
(2011)
Biophys. J.
, vol.101
, pp. 160-166
-
-
Sela, I.1
Lukatsky, D.2
-
17
-
-
84885125626
-
Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites
-
Afek, A. and Lukatsky, D.B. (2013) Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites. Biophys. J., 105, 1653-1660.
-
(2013)
Biophys. J.
, vol.105
, pp. 1653-1660
-
-
Afek, A.1
Lukatsky, D.B.2
-
18
-
-
84874901264
-
Genome-wide organization of eukaryotic preinitiation complex is influenced by nonconsensus protein-DNA binding
-
Afek, A. and Lukatsky, D. (2013) Genome-wide organization of eukaryotic preinitiation complex is influenced by nonconsensus protein-DNA binding. Biophys. J., 104, 1107-1115.
-
(2013)
Biophys. J
, vol.104
, pp. 1107-1115
-
-
Afek, A.1
Lukatsky, D.2
-
19
-
-
77950519937
-
Origins of specificity in protein-DNA recognition
-
Rohs, R., Jin, X., West, S.M., Joshi, R., Honig, B. and Mann, R.S. (2010) Origins of specificity in protein-DNA recognition. Annu. Rev. Biochem., 79, 233.
-
(2010)
Annu. Rev. Biochem
, vol.79
, pp. 233
-
-
Rohs, R.1
Jin, X.2
West, S.M.3
Joshi, R.4
Honig, B.5
Mann, R.S.6
-
20
-
-
80053441923
-
Dynamic protein-DNA recognition: Beyond what can be seen
-
Fuxreiter, M., Simon, I. and Bondos, S. (2011) Dynamic protein-DNA recognition: beyond what can be seen. Trends Biochem. Sci., 36, 415-423.
-
(2011)
Trends Biochem. Sci.
, vol.36
, pp. 415-423
-
-
Fuxreiter, M.1
Simon, I.2
Bondos, S.3
-
21
-
-
84874828227
-
Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy
-
Anderson, K.M., Esadze, A., Manoharan, M., Bru schweiler, R., Gorenstein, D.G. and Iwahara, J. (2013) Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy. J. Am. Chem. Soc., 135, 3613-3619.
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 3613-3619
-
-
Anderson, K.M.1
Esadze, A.2
Manoharan, M.3
Bru schweiler, R.4
Gorenstein, D.G.5
Iwahara, J.6
-
22
-
-
84896701049
-
NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins
-
Zandarashvili, L., Esadze, A. and Iwahara, J. (2013) NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins. Adv. Protein Chem. Struct. Biol., 93, 37-80.
-
(2013)
Adv. Protein Chem. Struct. Biol
, vol.93
, pp. 37-80
-
-
Zandarashvili, L.1
Esadze, A.2
Iwahara, J.3
-
23
-
-
84922442279
-
Temperature dependence of internal motions of protein side-chain NH3+ groups: Insight into energy barriers for transient breakage of hydrogen bonds
-
Zandarashvili, L. and Iwahara, J. (2014) Temperature dependence of internal motions of protein side-chain NH3+ groups: insight into energy barriers for transient breakage of hydrogen bonds. Biochemistry, 54, 538-545.
-
(2014)
Biochemistry
, vol.54
, pp. 538-545
-
-
Zandarashvili, L.1
Iwahara, J.2
-
24
-
-
79851490872
-
Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H-15N NMR spectroscopy
-
Esadze, A., Li, D.W., Wang, T., Br üschweiler, R. and Iwahara, J. (2011) Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H-15N NMR spectroscopy. J. Am. Chem. Soc., 133, 909-919.
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 909-919
-
-
Esadze, A.1
Li, D.W.2
Wang, T.3
Br üschweiler, R.4
Iwahara, J.5
-
25
-
-
84937154958
-
Dynamic equilibria of short-range electrostatic interactions at molecular interfaces of protein-DNA complexes
-
Chen, C., Esadze, A., Zandarashvili, L., Nguyen, D., Pettitt, B.M. and Iwahara, J. (2015) Dynamic equilibria of short-range electrostatic interactions at molecular interfaces of protein-DNA complexes. J. Phys. Chem. Lett., 6, 2733-2737.
-
(2015)
J. Phys. Chem. Lett
, vol.6
, pp. 2733-2737
-
-
Chen, C.1
Esadze, A.2
Zandarashvili, L.3
Nguyen, D.4
Pettitt, B.M.5
Iwahara, J.6
-
26
-
-
84880923011
-
A comprehensive model for the recognition of human telomeres by TRF1
-
Garton, M. and Laughton, C. (2013) A comprehensive model for the recognition of human telomeres by TRF1. J. Mol. Biol., 425, 2910-2921.
-
(2013)
J. Mol. Biol
, vol.425
, pp. 2910-2921
-
-
Garton, M.1
Laughton, C.2
-
27
-
-
0035661846
-
High-speed molecular mechanics searches for optimal DNA interaction sites
-
Lafontaine, I. and Lavery, R. (2001) High-speed molecular mechanics searches for optimal DNA interaction sites. Comb. Chem. High Throughput Screen., 4, 707-717.
-
(2001)
Comb. Chem. High Throughput Screen
, vol.4
, pp. 707-717
-
-
Lafontaine, I.1
Lavery, R.2
-
28
-
-
1642452665
-
Analyzing protein-DNA recognition mechanisms
-
Paillard, G. and Lavery, R. (2004) Analyzing protein-DNA recognition mechanisms. Structure, 12, 113-122.
-
(2004)
Structure
, vol.12
, pp. 113-122
-
-
Paillard, G.1
Lavery, R.2
-
29
-
-
44649194038
-
Protein-DNA recognition: Breaking the combinatorial barrier
-
Deremble, C., Lavery, R. and Zakrzewska, K. (2008) Protein-DNA recognition: Breaking the combinatorial barrier. Comput. Phys. Commun., 179, 112-119.
-
(2008)
Comput. Phys. Commun
, vol.179
, pp. 112-119
-
-
Deremble, C.1
Lavery, R.2
Zakrzewska, K.3
-
30
-
-
70450273194
-
Protein-DNA binding specificity: A grid-enabled computational approach applied to single and multiple protein assemblies
-
Zakrzewska, K., Bouvier, B., Michon, A., Blanchet, C. and Lavery, R. (2009) Protein-DNA binding specificity: A grid-enabled computational approach applied to single and multiple protein assemblies. Phys. Chem. Chem. Phys., 11, 10712-10721.
-
(2009)
Phys. Chem. Chem. Phys
, vol.11
, pp. 10712-10721
-
-
Zakrzewska, K.1
Bouvier, B.2
Michon, A.3
Blanchet, C.4
Lavery, R.5
-
31
-
-
0025250731
-
Genetic evidence equating SRY and the testis-determining factor
-
Berta, P., Hawkins, J.B., Sinclair, A.H., Taylor, A., Griffiths, B.L., Goodfellow, P.N. and Fellous, M. (1990) Genetic evidence equating SRY and the testis-determining factor. Nature, 348, 448-450.
-
(1990)
Nature
, vol.348
, pp. 448-450
-
-
Berta, P.1
Hawkins, J.B.2
Sinclair, A.H.3
Taylor, A.4
Griffiths, B.L.5
Goodfellow, P.N.6
Fellous, M.7
-
32
-
-
0035929239
-
Structural basis for SRY-dependent 46-x, Y sex reversal: Modulation of DNA bending by a naturally occurring point mutation
-
Murphy, E.C., Zhurkin, V.B., Louis, J.M., Cornilescu, G. and Clore, G.M. (2001) Structural basis for SRY-dependent 46-X, Y sex reversal: Modulation of DNA bending by a naturally occurring point mutation. J. Mol. Biol., 312, 481-499.
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 481-499
-
-
Murphy, E.C.1
Zhurkin, V.B.2
Louis, J.M.3
Cornilescu, G.4
Clore, G.M.5
-
33
-
-
0026529831
-
Skn-1, a maternally expressed gene required to specify the fate of ventral blastomeres in the early C. Elegans embryo
-
Bowerman, B., Eaton, B.A. and Priess, J.R. (1992) skn-1, a maternally expressed gene required to specify the fate of ventral blastomeres in the early C. elegans embryo. Cell, 68, 1061-1075.
-
(1992)
Cell
, vol.68
, pp. 1061-1075
-
-
Bowerman, B.1
Eaton, B.A.2
Priess, J.R.3
-
34
-
-
0027209420
-
The maternal gene skn-1 encodes a protein that is distributed unequally in early C. Elegans embryos
-
Bowerman, B., Draper, B.W., Mello, C.C. and Priess, J.R. (1993) The maternal gene skn-1 encodes a protein that is distributed unequally in early C. elegans embryos. Cell, 74, 443-452.
-
(1993)
Cell
, vol.74
, pp. 443-452
-
-
Bowerman, B.1
Draper, B.W.2
Mello, C.C.3
Priess, J.R.4
-
35
-
-
0031749528
-
A new DNA-binding motif in the skn-1 binding domain-DNA complex
-
Rupert, P.B., Daughdrill, G.W., Bowerman, B. and Matthews, B.W. (1998) A new DNA-binding motif in the Skn-1 binding domain-DNA complex. Nat. Struct. Biol., 5, 484-491.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 484-491
-
-
Rupert, P.B.1
Daughdrill, G.W.2
Bowerman, B.3
Matthews, B.W.4
-
36
-
-
0032913571
-
The SKN-1 amino- Terminal arm is a DNA specificity segment
-
Kophengnavong, T., Carroll, A.S. and Blackwell, T.K. (1999) The SKN-1 amino- Terminal arm is a DNA specificity segment. Mol. Cell. Biol., 19, 3039-3050.
-
(1999)
Mol. Cell. Biol
, vol.19
, pp. 3039-3050
-
-
Kophengnavong, T.1
Carroll, A.S.2
Blackwell, T.K.3
-
37
-
-
0028104274
-
Formation of a monomeric DNA binding domain by skn-1 bZIP and homeodomain elements
-
Blackwell, T.K., Bowerman, B. and Weintraub, H. (1994) Formation of a monomeric DNA binding domain by Skn-1 bZIP and homeodomain elements. Science, 266, 621-628.
-
(1994)
Science
, vol.266
, pp. 621-628
-
-
Blackwell, T.K.1
Bowerman, B.2
Weintraub, H.3
-
38
-
-
70350625466
-
Condition- Adapted stress and longevity gene regulation by caenorhabditis elegans SKN-1/NRF
-
Oliveira, R.P., Abate, J.P., Dilks, K., Landis, J., Ashraf, J., Murphy, C.T. and Blackwell, T.K. (2009) Condition- Adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf. Aging Cell, 8, 524-541.
-
(2009)
Aging Cell
, vol.8
, pp. 524-541
-
-
Oliveira, R.P.1
Abate, J.P.2
Dilks, K.3
Landis, J.4
Ashraf, J.5
Murphy, C.T.6
Blackwell, T.K.7
-
39
-
-
84875999410
-
The conserved SKN-1/Nrf2 stress response pathway regulates synaptic function in caenorhabditis elegans
-
Staab, T.A., Griffen, T.C., Corcoran, C., Evgrafov, O., Knowles, J.A. and Sieburth, D. (2013) The conserved SKN-1/Nrf2 stress response pathway regulates synaptic function in Caenorhabditis elegans. PLoS Genet., 9, e1003354.
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003354
-
-
Staab, T.A.1
Griffen, T.C.2
Corcoran, C.3
Evgrafov, O.4
Knowles, J.A.5
Sieburth, D.6
-
40
-
-
1242346370
-
The missing term in effective pair potentials
-
Berendsen, H.J.C., Grigera, J.R. and Straatsma, T.P. (1987) The missing term in effective pair potentials. J. Phys. Chem., 91, 6269-6271.
-
(1987)
J. Phys. Chem
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.J.C.1
Grigera, J.R.2
Straatsma, T.P.3
-
41
-
-
0029633186
-
Amber, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., DeBolt, S., Ferguson, D., Seibel, G. and Kollman, P. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun., 91, 1-41.
-
(1995)
Comput. Phys. Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
De Bolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
42
-
-
23444454552
-
The amber biomolecular simulation programs
-
Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B. and Woods, R.J. (2005) The Amber biomolecular simulation programs. J. Comput. Chem., 26, 1668-1688.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
43
-
-
0032922174
-
A modified version of the cornell et al. Force field with improved sugar pucker phases and helical repeat
-
Cheatham, T.E. 3rd, Cieplak, P. and Kollman, P.A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn., 16, 845-862.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 845-862
-
-
Cheatham, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
44
-
-
34250318638
-
Refinement of the amber force field for nucleic acids: Improving the description of alpha/gamma conformers
-
Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A. and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Pérez, A.1
Marchán, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
45
-
-
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
-
46
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H. and Pedersen, L.G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys., 103, 8577-8593.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
47
-
-
0033104039
-
New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations
-
Darden, T., Perera, L., Li, L. and Pedersen, L. (1999) New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure, 7, R55-R60.
-
(1999)
Structure
, vol.7
, pp. R55-R60
-
-
Darden, T.1
Perera, L.2
Li, L.3
Pedersen, L.4
-
48
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. and Haak, J.R. (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.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
49
-
-
33646940952
-
Numerical-integration of cartesian equations of motion of a system with constraints - molecular-dynamics of N- Alkanes
-
Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes. J. Comput. Phys., 23, 327-341.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
50
-
-
70450261721
-
Conformational analysis of nucleic acids revisited: Curves+
-
Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K. (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res., 37, 5917-5929.
-
(2009)
Nucleic Acids, Res.
, vol.37
, pp. 5917-5929
-
-
Lavery, R.1
Moakher, M.2
Maddocks, J.H.3
Petkeviciute, D.4
Zakrzewska, K.5
-
51
-
-
84903957372
-
Analyzing ion distributions around DNA
-
Lavery, R., Maddocks, J.H., Pasi, M. and Zakrzewska, K. (2014) Analyzing ion distributions around DNA. Nucleic Acids Res., 42, 8138-8149.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 8138-8149
-
-
Lavery, R.1
Maddocks, J.H.2
Pasi, M.3
Zakrzewska, K.4
-
52
-
-
84941073491
-
Analyzing ion distributions around DNA: Sequence-dependence of potassium ion distributions from microsecond molecular dynamics
-
Pasi, M., Maddocks, J.H. and Lavery, R. (2015) Analyzing ion distributions around DNA: Sequence-dependence of potassium ion distributions from microsecond molecular dynamics. Nucleic Acids Res., 43, 2413-2423.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 2413-2423
-
-
Pasi, M.1
Maddocks, J.H.2
Lavery, R.3
-
53
-
-
84936957551
-
-
Case, D.A., Berryman, J., Betz, R.M., Cerutti, D., Cheatham, T. III, Darden, T., Duke, R., Glese, T., Gohlke, H. et al. (2015) AMBER 2015.
-
(2015)
AMBER 2015
-
-
Case, D.A.1
Berryman, J.2
Betz, R.M.3
Cerutti, D.4
Cheatham, T.5
Darden, T.6
Duke, R.7
Glese, T.8
Gohlke, H.9
-
55
-
-
84944178665
-
Hierarchical grouping to optimize an objective function
-
Ward, J.H. Jr (1963) Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc., 58, 236-244.
-
(1963)
J Am. Stat. Assoc
, vol.58
, pp. 236-244
-
-
Ward, J.H.1
-
57
-
-
84919917563
-
Wards hierarchical agglomerative clustering method: Which algorithms implement wards criterion?
-
Murtagh, F. and Legendre, P. (2014) Wards hierarchical agglomerative clustering method: Which algorithms implement wards criterion? J. Classif., 31, 274-295.
-
(2014)
J. Classif
, vol.31
, pp. 274-295
-
-
Murtagh, F.1
Legendre, P.2
-
59
-
-
0029633162
-
JUMNA (junction minimization of nucleic- Acids)
-
Lavery, R., Zakrzewska, K. and Sklenar, H. (1995) JUMNA (Junction Minimization of Nucleic-Acids). Comput. Phys. Commun., 91, 135-158.
-
(1995)
Comput. Phys. Commun
, vol.91
, pp. 135-158
-
-
Lavery, R.1
Zakrzewska, K.2
Sklenar, H.3
-
60
-
-
2142738304
-
Weblogo: A sequence logo generator
-
Crooks, G.E., Hon, G., Chandonia, J.M. and Brenner, S.E. (2004) WebLogo: A sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
61
-
-
0022964809
-
Structure of the DNA-Eco RI endonuclease recognition complex at 3 a resolution
-
McClarin, J.A., Frederick, C.A., Wang, B.-C., Greene, P., Boyer, H.W., Grable, J. and Rosenberg, J.M. (1986) Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. Science, 234, 1526-1541.
-
(1986)
Science
, vol.234
, pp. 1526-1541
-
-
McClarin, J.A.1
Frederick, C.A.2
Wang, B.-C.3
Greene, P.4
Boyer, H.W.5
Grable, J.6
Rosenberg, J.M.7
-
62
-
-
0024294634
-
Crystal structure of TRP represser/operator complex at atomic resolution
-
Otwinowski, Z., Schevitz, R.W., Zhang, R.G., Lawson, C.L., Joachimiak, A., Marmorstein, R.Q., Luisi, B.F. and Sigler, P.B. (1988) Crystal structure of trp represser/operator complex at atomic resolution. Nature, 335, 321-329.
-
(1988)
Nature
, vol.335
, pp. 321-329
-
-
Otwinowski, Z.1
Schevitz, R.W.2
Zhang, R.G.3
Lawson, C.L.4
Joachimiak, A.5
Marmorstein, R.Q.6
Luisi, B.F.7
Sigler, P.B.8
-
63
-
-
84891808382
-
JASPAR 2014: An extensively expanded and updated open- Access database of transcription factor binding profiles
-
Mathelier, A., Zhao, X., Zhang, A.W., Parcy, F., Worsley-Hunt, R., Arenillas, D.J., Buchman, S., Chen, C.-Y., Chou, A. and Ienasescu, H. (2013) JASPAR 2014: An extensively expanded and updated open- Access database of transcription factor binding profiles. Nucleic Acids Res., 42, D142-D147.
-
(2013)
Nucleic Acids Res.
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
Buchman, S.7
Chen, C.-Y.8
Chou, A.9
Ienasescu, H.10
-
64
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E. et al. (2003) TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
-
65
-
-
0023042012
-
Information content of binding sites on nucleotide sequences
-
Schneider, T.D., Stormo, G.D., Gold, L. and Ehrenfeucht, A. (1986) Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415-431.
-
(1986)
J. Mol. Biol.
, vol.188
, pp. 415-431
-
-
Schneider, T.D.1
Stormo, G.D.2
Gold, L.3
Ehrenfeucht, A.4
-
66
-
-
84862908973
-
Nmr structure of a heterodimeric SAM: SAM complex: Characterization and manipulation of EphA2 binding reveal new cellular functions of SHIP2
-
Lee, H.J., Hota, P.K., Chugha, P., Guo, H., Miao, H., Zhang, L., Kim, S.-J., Stetzik, L., Wang, B.-C. and Buck, M. (2012) NMR structure of a heterodimeric SAM: SAM complex: characterization and manipulation of EphA2 binding reveal new cellular functions of SHIP2. Structure, 20, 41-55.
-
(2012)
Structure
, vol.20
, pp. 41-55
-
-
Lee, H.J.1
Hota, P.K.2
Chugha, P.3
Guo, H.4
Miao, H.5
Zhang, L.6
Kim, S.-J.7
Stetzik, L.8
Wang, B.-C.9
Buck, M.10
-
67
-
-
84887977883
-
Molecular simulations of a dynamic protein complex: Role of salt-bridges and polar interactions in configurational transitions
-
Zhang, L. and Buck, M. (2013) Molecular simulations of a dynamic protein complex: Role of salt-bridges and polar interactions in configurational transitions. Biophys. J., 105, 2412-2417.
-
(2013)
Biophys. J.
, vol.105
, pp. 2412-2417
-
-
Zhang, L.1
Buck, M.2
|