-
1
-
-
0347281686
-
Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E
-
Gross JD, Moerke NJ, von der Haar T, Lugovskoy AA, Sachs AB, et al. (2003) Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E. Cell 115: 739-750.
-
(2003)
Cell
, vol.115
, pp. 739-750
-
-
Gross, J.D.1
Moerke, N.J.2
von der Haar, T.3
Lugovskoy, A.A.4
Sachs, A.B.5
-
4
-
-
0842334536
-
Whither structural biology?
-
Harrison SC (2004) Whither structural biology? Nat Struct Mol Biol 11: 293-295.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 293-295
-
-
Harrison, S.C.1
-
5
-
-
0031244199
-
New trends in macromolecular X-ray crystallography
-
Wery JP, Schevitz RW (1997) New trends in macromolecular X-ray crystallography. Curr Op Chem Biol 1: 365-369.
-
(1997)
Curr Op Chem Biol
, vol.1
, pp. 365-369
-
-
Wery, J.P.1
Schevitz, R.W.2
-
6
-
-
33846285730
-
Solution NMR of large molecules and assemblies
-
Foster MP, McElroy CA, Amero CD (2007) Solution NMR of large molecules and assemblies. Biochemistry 46: 331-340.
-
(2007)
Biochemistry
, vol.46
, pp. 331-340
-
-
Foster, M.P.1
McElroy, C.A.2
Amero, C.D.3
-
7
-
-
44649180430
-
Challenges in design of biochemical assays for the identification of small molecules to target multiple conformations of protein kinases
-
Chene P (2008) Challenges in design of biochemical assays for the identification of small molecules to target multiple conformations of protein kinases. Drug Discov Today 13: 522-529.
-
(2008)
Drug Discov Today
, vol.13
, pp. 522-529
-
-
Chene, P.1
-
8
-
-
39149087014
-
Protein folding studied by single-molecule FRET
-
Schuler B, Eaton WA (2008) Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 18: 16-26.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 16-26
-
-
Schuler, B.1
Eaton, W.A.2
-
9
-
-
0342929614
-
Nonphysical sampling distributions in monte carlo free-energy estimation: Umbrella sampling
-
Torrie GM, Valleau JP (1977) Nonphysical sampling distributions in monte carlo free-energy estimation: Umbrella sampling. J Comput Phys 23: 187-199.
-
(1977)
J Comput Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
10
-
-
0037736706
-
Free energy calculations. the long and winding gilded road
-
Chipot C, Pearlman DA (2002) Free energy calculations. the long and winding gilded road. Molecular Simulation 28: 1-12.
-
(2002)
Molecular Simulation
, vol.28
, pp. 1-12
-
-
Chipot, C.1
Pearlman, D.A.2
-
11
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
Bolhuis PG, Chandler D, Dellago C, Geissler PL (2002) Transition path sampling: Throwing ropes over rough mountain passes, in the dark. Ann Rev Phys Chem 53: 291-318.
-
(2002)
Ann Rev Phys Chem
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
12
-
-
0028010888
-
HhaI methyltransferase flips its target base out of the DNA helix
-
Klimasauskas S, Kumar S, Roberts RJ, Cheng X (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76: 357-369.
-
(1994)
Cell
, vol.76
, pp. 357-369
-
-
Klimasauskas, S.1
Kumar, S.2
Roberts, R.J.3
Cheng, X.4
-
13
-
-
0034734377
-
Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base excision repair: The 3′ ends justify the means
-
Mol CD, Hosfield DJ, Tainer JA (2000) Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base excision repair: the 3′ ends justify the means. Mutat Res 460: 211-229.
-
(2000)
Mutat Res
, vol.460
, pp. 211-229
-
-
Mol, C.D.1
Hosfield, D.J.2
Tainer, J.A.3
-
14
-
-
4143149415
-
Site-Specific DNA Damage Recognition by Enzyme-Induced Base Flipping
-
Stivers JT (2004) Site-Specific DNA Damage Recognition by Enzyme-Induced Base Flipping. Prog Nucleic Acid Res Mol Biol 77: 37-65.
-
(2004)
Prog Nucleic Acid Res Mol Biol
, vol.77
, pp. 37-65
-
-
Stivers, J.T.1
-
15
-
-
0023256126
-
A single mode of DNA base-pair opening drives imino proton exchange
-
Gueron M, Kochoyan M, Leroy JL (1987) A single mode of DNA base-pair opening drives imino proton exchange. Nature 328: 89-92.
-
(1987)
Nature
, vol.328
, pp. 89-92
-
-
Gueron, M.1
Kochoyan, M.2
Leroy, J.L.3
-
16
-
-
0024292414
-
Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton
-
Leroy JL, Kochoyan M, Huynh-Dinh T, Gueron M (1988) Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton. J Mol Biol 200: 223-238.
-
(1988)
J Mol Biol
, vol.200
, pp. 223-238
-
-
Leroy, J.L.1
Kochoyan, M.2
Huynh-Dinh, T.3
Gueron, M.4
-
17
-
-
0036306053
-
Free energy and structural pathways of base flipping in a DNA GCGC containing sequence
-
Banavali NK, MacKerell Jr AD (2002) Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J Mol Biol 319: 141-160.
-
(2002)
J Mol Biol
, vol.319
, pp. 141-160
-
-
Banavali, N.K.1
MacKerell Jr, A.D.2
-
18
-
-
33745471427
-
Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix
-
Banavali NK, Huang N, MacKerell Jr AD (2006) Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. J Phys Chem B 110: 10997-11004.
-
(2006)
J Phys Chem B
, vol.110
, pp. 10997-11004
-
-
Banavali, N.K.1
Huang, N.2
MacKerell Jr, A.D.3
-
19
-
-
33644622321
-
Computational approaches for investigating base flipping in oligonucleotides
-
Priyakumar UD, MacKerell Jr AD (2006) Computational approaches for investigating base flipping in oligonucleotides. Chem Rev 106: 489-505.
-
(2006)
Chem Rev
, vol.106
, pp. 489-505
-
-
Priyakumar, U.D.1
MacKerell Jr, A.D.2
-
20
-
-
33745469232
-
Base flipping in a GCGC containing DNA dodecamer: A comparative study of the performance of the nucleic acid force fields, CHARMM, AMBER, and BMS
-
Priyakumar UD, MacKerell Jr AD (2006) Base flipping in a GCGC containing DNA dodecamer: A comparative study of the performance of the nucleic acid force fields, CHARMM, AMBER, and BMS. J Chem Theory Comput 2: 187-200.
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 187-200
-
-
Priyakumar, U.D.1
MacKerell Jr, A.D.2
-
21
-
-
31444443924
-
NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases
-
Priyakumar UD, MacKerell Jr AD (2006) NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases. J Am Chem Soc 128: 678-679.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 678-679
-
-
Priyakumar, U.D.1
MacKerell Jr, A.D.2
-
24
-
-
0345529861
-
C5-methylation of cytosine in B-DNA thermodynamically and kinetically stabilizes BI
-
Rauch C, Trieb M, Wellenzohn B, Loferer M, Voegele A, et al. (2003) C5-methylation of cytosine in B-DNA thermodynamically and kinetically stabilizes BI. J Am Chem Soc 125: 14990-14991.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 14990-14991
-
-
Rauch, C.1
Trieb, M.2
Wellenzohn, B.3
Loferer, M.4
Voegele, A.5
-
25
-
-
18644368600
-
The free energy landscape of A-DNA to B-DNA conversion in aqueous solution
-
Banavali NK, Roux B (2005) The free energy landscape of A-DNA to B-DNA conversion in aqueous solution. J Am Chem Soc 127: 6866-6876.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 6866-6876
-
-
Banavali, N.K.1
Roux, B.2
-
26
-
-
7744233282
-
Opening Mechanism of G.T/U Pairs in DNA and RNA duplexes: A Combined Study of Imino Proton Exchange and Molecular Dynamics Simulation
-
Varnai P, Canalia M, Leroy JL (2004) Opening Mechanism of G.T/U Pairs in DNA and RNA duplexes: A Combined Study of Imino Proton Exchange and Molecular Dynamics Simulation. J Am Chem Soc 126: 14659-14667.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 14659-14667
-
-
Varnai, P.1
Canalia, M.2
Leroy, J.L.3
-
28
-
-
0015511563
-
Conformational analysis of sugar ring in nucleosides and nucleotides - new description using concept of pseudorotation
-
Altona C, Sundaralingam M (1972) Conformational analysis of sugar ring in nucleosides and nucleotides - new description using concept of pseudorotation. J Am Chem Soc 94: 8205-8206.
-
(1972)
J Am Chem Soc
, vol.94
, pp. 8205-8206
-
-
Altona, C.1
Sundaralingam, M.2
-
29
-
-
0035850731
-
A standard reference frame for the description of nucleic acid base-pair geometry
-
Olson W, Bansal M, Burley SK, Dickerson RE, Gerstein M, et al. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J Mol Biol 313: 299-237.
-
(2001)
J Mol Biol
, vol.313
, pp. 299-237
-
-
Olson, W.1
Bansal, M.2
Burley, S.K.3
Dickerson, R.E.4
Gerstein, M.5
-
30
-
-
0000335508
-
Conformational properties of the deoxyribose and ribose moieties of nucleic acids: A quantum mechanical study
-
Foloppe N, MacKerell Jr AD (1998) Conformational properties of the deoxyribose and ribose moieties of nucleic acids: A quantum mechanical study. J Phys Chem B 102: 6669-6678.
-
(1998)
J Phys Chem B
, vol.102
, pp. 6669-6678
-
-
Foloppe, N.1
MacKerell Jr, A.D.2
-
31
-
-
0035584142
-
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation
-
Schneider T (2001) Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation. Nucleic Acids Res 29: 4881-4891.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 4881-4891
-
-
Schneider, T.1
-
32
-
-
0034694685
-
Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (cytosine C5)-methyltransferase
-
Wang PY, Brank AS, Banavali NK, Nicklaus MC, Marquez VE, et al. (2000) Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (cytosine C5)-methyltransferase. J Am Chem Soc 122: 12422-12434.
-
(2000)
J Am Chem Soc
, vol.122
, pp. 12422-12434
-
-
Wang, P.Y.1
Brank, A.S.2
Banavali, N.K.3
Nicklaus, M.C.4
Marquez, V.E.5
-
33
-
-
3242714355
-
Caught in the act: Visualization of an intermediate in the DNA base-flipping pathway induced by Hhal methyltransferase
-
Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, et al. (2004) Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by Hhal methyltransferase. Nucleic Acids Res 32: 3877-3886.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 3877-3886
-
-
Horton, J.R.1
Ratner, G.2
Banavali, N.K.3
Huang, N.4
Choi, Y.5
-
34
-
-
0346456880
-
Experimental and structural evidence that herpes 1 kinase and cellular DNA polymerase(s) discriminate on the basis of sugar pucker
-
Marquez VE, Ben-Kasus T, Barchi JJ, Green KM, Nicklaus MC, et al. Experimental and structural evidence that herpes 1 kinase and cellular DNA polymerase(s) discriminate on the basis of sugar pucker. J Am Chem Soc 126: 543-549.
-
J Am Chem Soc
, vol.126
, pp. 543-549
-
-
Marquez, V.E.1
Ben-Kasus, T.2
Barchi, J.J.3
Green, K.M.4
Nicklaus, M.C.5
-
35
-
-
0001549017
-
Contribution of the phosphodiester backbone and glycosyl linkage intrinsic torsional energetics to DNA structure and dynamics
-
Foloppe N, MacKerell Jr AD (1999) Contribution of the phosphodiester backbone and glycosyl linkage intrinsic torsional energetics to DNA structure and dynamics. J Phys Chem B 103: 10955-10964.
-
(1999)
J Phys Chem B
, vol.103
, pp. 10955-10964
-
-
Foloppe, N.1
MacKerell Jr, A.D.2
-
36
-
-
0030071775
-
Geometric parameters in nucleic acids: Sugar and phosphate constituents
-
Gelbin A, Schneider B, Clowney L, Hsieh SH, Olson WK, et al. (1996) Geometric parameters in nucleic acids: Sugar and phosphate constituents. J Am Chem Soc 118: 519-529.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 519-529
-
-
Gelbin, A.1
Schneider, B.2
Clowney, L.3
Hsieh, S.H.4
Olson, W.K.5
-
37
-
-
0031195002
-
Conformations of the sugar-phosphate backbone in helical DNA crystal structures
-
Schneider B, Neidle S, Berman HM (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42: 113-124.
-
(1997)
Biopolymers
, vol.42
, pp. 113-124
-
-
Schneider, B.1
Neidle, S.2
Berman, H.M.3
-
38
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Lu XJ, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31: 5108-5121.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5108-5121
-
-
Lu, X.J.1
Olson, W.K.2
-
39
-
-
0000202448
-
Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13 = C14 and C15 = N16 bonds in the retinal of bacteriorhodopsin
-
Crouzy S, Baudry J, Smith JC, Roux B (1999) Efficient calculation of two-dimensional adiabatic and free energy maps: application to the isomerization of the C13 = C14 and C15 = N16 bonds in the retinal of bacteriorhodopsin. J Comput Chem 20: 1644-1658.
-
(1999)
J Comput Chem
, vol.20
, pp. 1644-1658
-
-
Crouzy, S.1
Baudry, J.2
Smith, J.C.3
Roux, B.4
-
40
-
-
0037850968
-
Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI
-
Edgell DR, Stanger MJ, Belfort M (2003) Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI. Curr Biol 13: 973-978.
-
(2003)
Curr Biol
, vol.13
, pp. 973-978
-
-
Edgell, D.R.1
Stanger, M.J.2
Belfort, M.3
-
41
-
-
16644366643
-
Differences between EcoRI nonspecific and star sequence complexes revealed by osmotic stress
-
Sidorova NY, Rau DC (2005) Differences between EcoRI nonspecific and star sequence complexes revealed by osmotic stress. Biophys J 87: 2564-2576.
-
(2005)
Biophys J
, vol.87
, pp. 2564-2576
-
-
Sidorova, N.Y.1
Rau, D.C.2
-
42
-
-
34247189120
-
Quantitative Conformationally Sampled Pharmacophore for δ Opioid Ligands: Reevaluation of Hydrophobic Moieties Essential for Biological Activity
-
Bernard D, Coop A, MacKerell Jr AD (2007) Quantitative Conformationally Sampled Pharmacophore for δ Opioid Ligands: Reevaluation of Hydrophobic Moieties Essential for Biological Activity. J Med Chem 50: 1799-1809.
-
(2007)
J Med Chem
, vol.50
, pp. 1799-1809
-
-
Bernard, D.1
Coop, A.2
MacKerell Jr, A.D.3
-
43
-
-
0037178070
-
Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations
-
Varnai P, Lavery R (2002) Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations. J Am Chem Soc 124: 7272-7273.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 7272-7273
-
-
Varnai, P.1
Lavery, R.2
-
44
-
-
0037422594
-
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase
-
Huang N, Banavali NK, MacKerell Jr AD (2003) Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc Natl Acad Sci U S A 100: 68-73.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 68-73
-
-
Huang, N.1
Banavali, N.K.2
MacKerell Jr, A.D.3
-
45
-
-
0001427619
-
CHARMM - a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 21: 105-120.
-
(1983)
J Comput Chem
, vol.21
, pp. 105-120
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
-
46
-
-
0242593434
-
Development and current status of the CHARMM force field for nucleic acids
-
Mackerell Jr AD, Banavali NK, Foloppe N (2000) Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56: 257-265.
-
(2000)
Biopolymers
, vol.56
, pp. 257-265
-
-
Mackerell Jr, A.D.1
Banavali, N.K.2
Foloppe, N.3
-
47
-
-
0000214231
-
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
-
Mackerell Jr AD, Banavali NK (2000) All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J Comput Chem 21: 105-120.
-
(2000)
J Comput Chem
, vol.21
, pp. 105-120
-
-
Mackerell Jr, A.D.1
Banavali, N.K.2
-
48
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79: 926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
49
-
-
65849500894
-
Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
-
Beglov D, Roux B (1994) Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations. J Chem Phys 98: 10089-10092.
-
(1994)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Beglov, D.1
Roux, B.2
-
50
-
-
33846823909
-
Particle Mesh Ewald - an N.log(N) method for Ewald sums in large systems
-
Darden T, York D, 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
-
51
-
-
36449007836
-
Constant pressure molecular dynamics simulation - the Langevin piston method
-
Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation - the Langevin piston method. J Chem Phys 103: 4613-4621.
-
(1995)
J Chem Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Pastor, R.W.3
Brooks, B.R.4
-
52
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules .1. The method
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The weighted histogram analysis method for free-energy calculations on biomolecules .1. The method. J Comput Chem 13: 1011-1021.
-
(1992)
J Comput Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
53
-
-
0035277126
-
Extension to the weighted histogram analysis method: Combining umbrella sampling with free energy calculations
-
Souaille M, Roux B (2001) Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Comput Phys Comm 135: 40-57.
-
(2001)
Comput Phys Comm
, vol.135
, pp. 40-57
-
-
Souaille, M.1
Roux, B.2
-
54
-
-
0032522139
-
DNA bending: The prevalence of kinkiness and the virtues of normality
-
Dickerson RE (1998) DNA bending: The prevalence of kinkiness and the virtues of normality. Nucleic Acids Res 26: 1906-1926.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1906-1926
-
-
Dickerson, R.E.1
|