-
1
-
-
0029871812
-
Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae
-
Caponigro G, Parker R. Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae. Microbiol Rev 1996;60:233-249.
-
(1996)
Microbiol Rev
, vol.60
, pp. 233-249
-
-
Caponigro, G.1
Parker, R.2
-
2
-
-
0035371050
-
5′-Terminal cap structure in eukaryotic messenger ribonucleic-acids
-
Mitchell P, Tollervey D. 5′-Terminal cap structure in eukaryotic messenger ribonucleic-acids. Curr Opin Cell Biol 2001;13:320-325.
-
(2001)
Curr Opin Cell Biol
, vol.13
, pp. 320-325
-
-
Mitchell, P.1
Tollervey, D.2
-
4
-
-
0019276997
-
5′-terminal cap structure in eucaryotic messenger ribonucleic acids
-
Banerjee AK. 5′-terminal cap structure in eucaryotic messenger ribonucleic acids. Microbiol Rev 1980;44:175-205.
-
(1980)
Microbiol Rev
, vol.44
, pp. 175-205
-
-
Banerjee, A.K.1
-
5
-
-
0029441923
-
The influence of 5′ and 3′ end structures on pre-mRNA metabolism
-
Lewis JD, Gunderson SI, Mattaj IW. The influence of 5′ and 3′ end structures on pre-mRNA metabolism. J Cell Sci Suppl 1995;19:13-19.
-
(1995)
J Cell Sci Suppl
, vol.19
, pp. 13-19
-
-
Lewis, J.D.1
Gunderson, S.I.2
Mattaj, I.W.3
-
6
-
-
0037117760
-
Mammalian mRNA degradation: Beginning at the end
-
van Hoof A, Parker R. Mammalian mRNA degradation: beginning at the end. Curr Biol 2002;12:R285-R287.
-
(2002)
Curr Biol
, vol.12
-
-
van Hoof, A.1
Parker, R.2
-
7
-
-
0742288008
-
The enzymes and control of eukaryotic mRNA turnover
-
Parker R, Song H. The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 2004;11:121-127.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 121-127
-
-
Parker, R.1
Song, H.2
-
8
-
-
0037009517
-
The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases
-
Liu HD, Rodgers ND, Jiao X, Kiledjian M. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J 2002;21:4699-4708.
-
(2002)
EMBO J
, vol.21
, pp. 4699-4708
-
-
Liu, H.D.1
Rodgers, N.D.2
Jiao, X.3
Kiledjian, M.4
-
10
-
-
0035861864
-
Functional link between the mammalian exosome and mRNA decapping
-
Wang Z, Kiledjian M. Functional link between the mammalian exosome and mRNA decapping. Cell 2001;107:751-762.
-
(2001)
Cell
, vol.107
, pp. 751-762
-
-
Wang, Z.1
Kiledjian, M.2
-
11
-
-
4344641442
-
Functional analysis of mRNA scavenger decapping enzymes
-
Liu SW, Jiao XF, Liu HD, Gu MG, Lima CD, Kiledjian M. Functional analysis of mRNA scavenger decapping enzymes. RNA 2004;10:1412-1422.
-
(2004)
RNA
, vol.10
, pp. 1412-1422
-
-
Liu, S.W.1
Jiao, X.F.2
Liu, H.D.3
Gu, M.G.4
Lima, C.D.5
Kiledjian, M.6
-
12
-
-
0142027794
-
DcpS can act in the 5′-3′ mRNA decay pathway in addition to the 3′-5′ pathway
-
van Dijk E, Le Hir H, Seraphin B. DcpS can act in the 5′-3′ mRNA decay pathway in addition to the 3′-5′ pathway. Proc Natl Acad Sci USA 2003;100:12081-12086.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12081-12086
-
-
van Dijk, E.1
Le Hir, H.2
Seraphin, B.3
-
13
-
-
14844359631
-
Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping
-
Chen N, Walsh MA, Liu YY, Parker R, Song HW. Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. J Mol Biol 2005;347:707-718.
-
(2005)
J Mol Biol
, vol.347
, pp. 707-718
-
-
Chen, N.1
Walsh, M.A.2
Liu, Y.Y.3
Parker, R.4
Song, H.W.5
-
14
-
-
1842816418
-
Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity
-
Gu MG, Fabrega C, Liu SW, Liu HD, Kiledjian M, Lima CD. Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity. Mol Cell 2004;14:67-80.
-
(2004)
Mol Cell
, vol.14
, pp. 67-80
-
-
Gu, M.G.1
Fabrega, C.2
Liu, S.W.3
Liu, H.D.4
Kiledjian, M.5
Lima, C.D.6
-
15
-
-
0020647920
-
Functional significance of flexibility in proteins
-
Huber R, Bennett WS Jr. Functional significance of flexibility in proteins. Biopolymers 1983;22:261-279.
-
(1983)
Biopolymers
, vol.22
, pp. 261-279
-
-
Huber, R.1
Bennett Jr., W.S.2
-
16
-
-
18744371588
-
Chemical theory and computation special feature: Molecular dynamics and protein function
-
Karplus M, Kuriyan J. Chemical theory and computation special feature: molecular dynamics and protein function. Proc Natl Acad Sci USA 2005;102:6679-6685.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6679-6685
-
-
Karplus, M.1
Kuriyan, J.2
-
17
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002;9:646-652.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
18
-
-
0020698476
-
Dynamics of proteins:. elements and function
-
Karplus M, McCammon JA. Dynamics of proteins:. elements and function. Annu Rev Biochem 1983;53:263-300.
-
(1983)
Annu Rev Biochem
, vol.53
, pp. 263-300
-
-
Karplus, M.1
McCammon, J.A.2
-
19
-
-
33846413566
-
Conformational effects in enzyme catalysis: Reaction via a high energy conformation in fatty acid amide hydrolase
-
Lodola A, Mor M, Zurek J, Tarzia G, Piomelli D, Harvey JN, Mulholland AJ. Conformational effects in enzyme catalysis: reaction via a high energy conformation in fatty acid amide hydrolase. Biophys J 2007;92:L20-L22.
-
(2007)
Biophys J
, vol.92
-
-
Lodola, A.1
Mor, M.2
Zurek, J.3
Tarzia, G.4
Piomelli, D.5
Harvey, J.N.6
Mulholland, A.J.7
-
20
-
-
33645801770
-
Atomic description of an enzyme reaction dominated by proton tunneling
-
Masgrau L, Roujeinikova A, Johannissen LO, Hothi P, Basran J, Ranaghan KE, Mulholland AJ, Sutcliffe MJ, Scrutton NS, Leys D. Atomic description of an enzyme reaction dominated by proton tunneling. Science 2006;312:237-241.
-
(2006)
Science
, vol.312
, pp. 237-241
-
-
Masgrau, L.1
Roujeinikova, A.2
Johannissen, L.O.3
Hothi, P.4
Basran, J.5
Ranaghan, K.E.6
Mulholland, A.J.7
Sutcliffe, M.J.8
Scrutton, N.S.9
Leys, D.10
-
21
-
-
33644919954
-
Subtype selectivity and flexibility of ionotropic glutamate receptors upon ligand binding
-
Pentikäinen U, Settimo L, Johnson MS, Pentikäinen OT. Subtype selectivity and flexibility of ionotropic glutamate receptors upon ligand binding. Org Biomol Chem 2006;4:1058-1070.
-
(2006)
Org Biomol Chem
, vol.4
, pp. 1058-1070
-
-
Pentikäinen, U.1
Settimo, L.2
Johnson, M.S.3
Pentikäinen, O.T.4
-
22
-
-
33645789373
-
The Fe-CO bond energy in myoglobin: A QM/MM study of the effect of tertiary structure
-
Strickland N, Mulholland AJ, Harvey JN. The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure. Biophys J 2006;90:L27-L29.
-
(2006)
Biophys J
, vol.90
-
-
Strickland, N.1
Mulholland, A.J.2
Harvey, J.N.3
-
23
-
-
0036285978
-
Molecular dynamics simulations of biological reactions
-
Warshel A. Molecular dynamics simulations of biological reactions. Acc Chem Res 2002;35:385-395.
-
(2002)
Acc Chem Res
, vol.35
, pp. 385-395
-
-
Warshel, A.1
-
24
-
-
0031922657
-
Conformational dynamics and enzyme activity
-
Yon JM, Perahia D, Ghelis C. Conformational dynamics and enzyme activity. Biochimie 1998;80:33-42.
-
(1998)
Biochimie
, vol.80
, pp. 33-42
-
-
Yon, J.M.1
Perahia, D.2
Ghelis, C.3
-
25
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
26
-
-
19944426826
-
BODIL: A molecular modeling environment for structure-function analysis and drug design
-
Lehtonen JV, Still DJ, Rantanen VV, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Repo S, Jussila A, Jaakkola J, Pentikäinen O, Nyrönen T, Salminen T, Gyllenberg M, Johnson M. BODIL: a molecular modeling environment for structure-function analysis and drug design. J Comput Aided Mol Des 2004;18:401-419.
-
(2004)
J Comput Aided Mol Des
, vol.18
, pp. 401-419
-
-
Lehtonen, J.V.1
Still, D.J.2
Rantanen, V.V.3
Ekholm, J.4
Björklund, D.5
Iftikhar, Z.6
Huhtala, M.7
Repo, S.8
Jussila, A.9
Jaakkola, J.10
Pentikäinen, O.11
Nyrönen, T.12
Salminen, T.13
Gyllenberg, M.14
Johnson, M.15
-
27
-
-
0029878720
-
VMD: Visual molecular dynamics. J Mol Graph
-
Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:27-28, 33-38.
-
(1996)
, vol.14
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
28
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
29
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe N, Mackerell A. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 2000;21:86-104.
-
(2000)
J Comput Chem
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
Mackerell, A.2
-
30
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madure JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madure, J.D.3
Impey, R.W.4
Klein, M.L.5
-
31
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin piston method
-
Feller SE, Zhang YH, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 1995;103:4613-4621.
-
(1995)
J Chem Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.H.2
Pastor, R.W.3
Brooks, B.R.4
-
32
-
-
85190282155
-
-
Schlick T, Skeel R, Brunger ATD, Kale LV, Board JA Jr, Hermans J, Schulte K. Computational modeling predicts the structure and ... computational molecular biophysics. J Comput Phys 1999;151:9-48.
-
Schlick T, Skeel R, Brunger ATD, Kale LV, Board JA Jr, Hermans J, Schulte K. Computational modeling predicts the structure and ... computational molecular biophysics. J Comput Phys 1999;151:9-48.
-
-
-
-
33
-
-
33846823909
-
Panicle mesh Ewald-an N.Log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L. Panicle mesh Ewald-an N.Log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
34
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995;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
-
35
-
-
0141465322
-
-
Pratt LR, Hummer G, editors. American Institute of Physics, Melville, New York
-
Sagui C, Darden TA. In Simulation and Theory of Electrostatic Interactions in Solution. In: Pratt LR, Hummer G, editors. American Institute of Physics, Melville, New York, 1999, pp. 104-113.
-
(1999)
In Simulation and Theory of Electrostatic Interactions in Solution
, pp. 104-113
-
-
Sagui, C.1
Darden, T.A.2
-
36
-
-
0034506266
-
-
Toukmaji A, Sagui C, Board J, Darden T. Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions. J Chem Phys 2000;113:10913-10927.
-
Toukmaji A, Sagui C, Board J, Darden T. Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions. J Chem Phys 2000;113:10913-10927.
-
-
-
-
37
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert J, Ciccotti G, Berendsen HJ. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.1
Ciccotti, G.2
Berendsen, H.J.3
-
38
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.
-
(1991)
J Appl Crystallogr
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
39
-
-
0030815133
-
Raster3D: Photorealistic molecular graphics
-
Merritt EA, Bacon DJ. Raster3D: photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.
-
(1997)
Methods Enzymol
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
Bacon, D.J.2
-
40
-
-
1942519384
-
Dynamic properties of the N-terminal swapped dimer of ribonuclease A
-
Merlino A, Vitagliano L, Ceruso MA, Mazzarella L. Dynamic properties of the N-terminal swapped dimer of ribonuclease A. Biophys J 2004;86:2383-2391.
-
(2004)
Biophys J
, vol.86
, pp. 2383-2391
-
-
Merlino, A.1
Vitagliano, L.2
Ceruso, M.A.3
Mazzarella, L.4
-
41
-
-
20444387408
-
Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A
-
Merlino A, Ceruso MA, Vitagliano L, Mazzarella L. Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A. Biophys J 2005;88:2003-2012.
-
(2005)
Biophys J
, vol.88
, pp. 2003-2012
-
-
Merlino, A.1
Ceruso, M.A.2
Vitagliano, L.3
Mazzarella, L.4
-
42
-
-
0027074883
-
Domain motions in phosphoglycerate kinase: Determination of interdomain distance distribution by site-specific labeling and time-resolved fluorescence energy transfer
-
Haran G, Haas E, Szpikowska BK, Mas MT. Domain motions in phosphoglycerate kinase: determination of interdomain distance distribution by site-specific labeling and time-resolved fluorescence energy transfer. Proc Natl Acad Sci USA 1992;89:11764-11768.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 11764-11768
-
-
Haran, G.1
Haas, E.2
Szpikowska, B.K.3
Mas, M.T.4
-
43
-
-
33746888705
-
Effects of ligand binding and oxidation on hinge-bending motions in S-adenosyl-L-homocysteine hydrolase
-
Wang M, Unruh JR, Johnson CK, Kuczera K, Schowen RL, Borchardt RT. Effects of ligand binding and oxidation on hinge-bending motions in S-adenosyl-L-homocysteine hydrolase. Biochemistry 2006;45:7778-7786.
-
(2006)
Biochemistry
, vol.45
, pp. 7778-7786
-
-
Wang, M.1
Unruh, J.R.2
Johnson, C.K.3
Kuczera, K.4
Schowen, R.L.5
Borchardt, R.T.6
-
44
-
-
37849005273
-
-
Wang M, Chen H, Unruh J, Johnson CR, Schowen RL, Borchadt RT, Kuchera K. Dynamics of proteins and macromolecular Assemblies 32nd Steenbock Symposium 2006.
-
(2006)
Dynamics of proteins and macromolecular Assemblies 32nd Steenbock Symposium
-
-
Wang, M.1
Chen, H.2
Unruh, J.3
Johnson, C.R.4
Schowen, R.L.5
Borchadt, R.T.6
Kuchera, K.7
-
45
-
-
0036108484
-
3D domain swapping: As domains continue to swap
-
Liu Y, Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci 2002;11:1285-1299.
-
(2002)
Protein Sci
, vol.11
, pp. 1285-1299
-
-
Liu, Y.1
Eisenberg, D.2
-
46
-
-
0037337270
-
The unfolding story of three-dimensional domain swapping
-
Rousseau F, Schymkowitz JWH, Itzhaki LS. The unfolding story of three-dimensional domain swapping. Structure 2003;11:243-251.
-
(2003)
Structure
, vol.11
, pp. 243-251
-
-
Rousseau, F.1
Schymkowitz, J.W.H.2
Itzhaki, L.S.3
|