-
1
-
-
0037058959
-
Investigation of viral DNA packaging using molecular mechanics models
-
J. Arsuaga, R.K.Z. Tan, M. Vazquez, D.W. Sumners, and S.C. Harvey Investigation of viral DNA packaging using molecular mechanics models Biophys. Chem. 101-102 2002 475 484
-
(2002)
Biophys. Chem.
, vol.101-102
, pp. 475-484
-
-
Arsuaga, J.1
Tan, R.K.Z.2
Vazquez, M.3
Sumners, D.W.4
Harvey, S.C.5
-
2
-
-
0038539610
-
2+ binding sites of the 5s rRNA loop e motif as investigated by molecular dynamics simulations
-
2+ binding sites of the 5s rRNA loop E motif as investigated by molecular dynamics simulations Chem. Biol. 10 2003 551 561
-
(2003)
Chem. Biol.
, vol.10
, pp. 551-561
-
-
Auffinger, P.1
Bielecki, L.2
Westhof, E.3
-
3
-
-
0033954256
-
The protein data bank
-
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The protein data bank Nucleic Acids Res. 28 2000 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
-
4
-
-
2642553698
-
Cowpea mosaic virus as a scaffold for 3-d patterning of gold nanoparticles
-
A.S. Blum, C.M. Soto, C.D. Wilson, J.D. Cole, M. Kim, B. Gnade, A. Chatterji, W.F. Ochoa, T. Lin, and J.E. Johnson Cowpea mosaic virus as a scaffold for 3-d patterning of gold nanoparticles Nano Lett. 4 2004 867 870
-
(2004)
Nano Lett.
, vol.4
, pp. 867-870
-
-
Blum, A.S.1
Soto, C.M.2
Wilson, C.D.3
Cole, J.D.4
Kim, M.5
Gnade, B.6
Chatterji, A.7
Ochoa, W.F.8
Lin, T.9
Johnson, J.E.10
-
6
-
-
0032707625
-
Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function
-
K. Chin, K.A. Sharp, B. Honig, and A.M. Pyle Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function Nat. Struct. Biol. 6 1999 1055 1061
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1055-1061
-
-
Chin, K.1
Sharp, K.A.2
Honig, B.3
Pyle, A.M.4
-
7
-
-
0030780581
-
Dissecting the roles of VP0 cleavage and RNA packaging in picornavirus capsid stabilization: The structure of empty capsids of foot-and-mouth disease virus
-
S. Curry, E. Fry, W. Blakemore, R. Abu-Ghazeleh, T. Jackson, A. King, S. Lea, J. Newman, and D. Stuart Dissecting the roles of VP0 cleavage and RNA packaging in picornavirus capsid stabilization: the structure of empty capsids of foot-and-mouth disease virus J. Virol. 71 1997 9743 9752
-
(1997)
J. Virol.
, vol.71
, pp. 9743-9752
-
-
Curry, S.1
Fry, E.2
Blakemore, W.3
Abu-Ghazeleh, R.4
Jackson, T.5
King, A.6
Lea, S.7
Newman, J.8
Stuart, D.9
-
8
-
-
0035039221
-
Biophysical studies on the RNA cores of satellite tobacco mosaic virus
-
J. Day, Y.G. Kuznetsov, S.B. Larson, A. Greenwood, and A. McPherson Biophysical studies on the RNA cores of satellite tobacco mosaic virus Biophys. J. 80 2001 2364 2371
-
(2001)
Biophys. J.
, vol.80
, pp. 2364-2371
-
-
Day, J.1
Kuznetsov, Y.G.2
Larson, S.B.3
Greenwood, A.4
McPherson, A.5
-
9
-
-
0031663951
-
Satellite tobacco mosaic virus
-
J.A. Dodds Satellite tobacco mosaic virus Annu. Rev. Phytopathol. 36 1998 295 310
-
(1998)
Annu. Rev. Phytopathol.
, vol.36
, pp. 295-310
-
-
Dodds, J.A.1
-
10
-
-
36449007836
-
Constant pressure molecular dynamics simulation - The Langevin piston method
-
S.E. Feller, Y.H. Zhang, R.W. Pastor, and B.R. Brooks Constant pressure molecular dynamics simulation - the Langevin piston method J. Chem. Phys. 103 1995 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
-
11
-
-
0027518457
-
Ordered duplex RNA controls capsid architecture in an icosahedral animal virus
-
A.J. Fisher, and J.E. Johnson Ordered duplex RNA controls capsid architecture in an icosahedral animal virus Nature 361 1993 176 179
-
(1993)
Nature
, vol.361
, pp. 176-179
-
-
Fisher, A.J.1
Johnson, J.E.2
-
12
-
-
0348244547
-
All-atom empirical force field for nucleic acids: 1) parameter optimization based on small molecule and condensed phase macromolecular target data
-
N. Foloppe, and A.D. MacKerell Jr. All-atom empirical force field for nucleic acids: 1) parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 21 2000 86 104
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell Jr., A.D.2
-
13
-
-
0035830964
-
Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations
-
S.L. Heilman-Miller, D. Thirumalai, and S.A. Woodson Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations J. Mol. Biol. 306 2001 1157 1166
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 1157-1166
-
-
Heilman-Miller, S.L.1
Thirumalai, D.2
Woodson, S.A.3
-
15
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 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
-
16
-
-
0030752557
-
The structure of alfalfa mosaic virus capsid protein assembled as a T = 1 icosahedral particle at 4.0 Å
-
A. Kumar, V. Reddy, V. Yusibov, P. Chipman, Y. Hata, I. Fita, K. Fukuyama, M. Rossmann, L. Loesch-Fries, and T. Baker The structure of alfalfa mosaic virus capsid protein assembled as a T = 1 icosahedral particle at 4.0 Å J. Virol. 71 1997 7911 7916
-
(1997)
J. Virol.
, vol.71
, pp. 7911-7916
-
-
Kumar, A.1
Reddy, V.2
Yusibov, V.3
Chipman, P.4
Hata, Y.5
Fita, I.6
Fukuyama, K.7
Rossmann, M.8
Loesch-Fries, L.9
Baker, T.10
-
17
-
-
14144252651
-
Atomic force microscopy analysis of icosahedral virus RNA
-
Y.G. Kuznetsov, S. Daijogo, J. Zhou, B.L. Semler, and A. McPherson Atomic force microscopy analysis of icosahedral virus RNA J. Mol. Biol. 347 2005 41 52
-
(2005)
J. Mol. Biol.
, vol.347
, pp. 41-52
-
-
Kuznetsov, Y.G.1
Daijogo, S.2
Zhou, J.3
Semler, B.L.4
McPherson, A.5
-
18
-
-
1242336964
-
Packaging double-helical DNA into viral capsids
-
J.C. LaMarque, T.V. Le, and S.C. Harvey Packaging double-helical DNA into viral capsids Biopolymers 73 2004 348 355
-
(2004)
Biopolymers
, vol.73
, pp. 348-355
-
-
Lamarque, J.C.1
Le, T.V.2
Harvey, S.C.3
-
19
-
-
0035252686
-
Satellite tobacco mosaic virus RNA: Structure and implications for assembly
-
S.B. Larson, and A. McPherson Satellite tobacco mosaic virus RNA: structure and implications for assembly Curr. Opin. Struct. Biol. 11 2001 59 65
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 59-65
-
-
Larson, S.B.1
McPherson, A.2
-
20
-
-
0032549663
-
Refined structure of satellite tobacco mosaic virus at 1.8 Å resolution
-
S.B. Larson, J. Day, A. Greenwood, and A. McPherson Refined structure of satellite tobacco mosaic virus at 1.8 Å resolution J. Mol. Biol. 277 1998 37 59
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 37-59
-
-
Larson, S.B.1
Day, J.2
Greenwood, A.3
McPherson, A.4
-
21
-
-
15244356570
-
The RNA of turnip yellow mosaic virus exhibits icosahedral order
-
S.B. Larson, R.W. Lucas, A. Greenwood, and A. McPherson The RNA of turnip yellow mosaic virus exhibits icosahedral order Virology 334 2005 245 254
-
(2005)
Virology
, vol.334
, pp. 245-254
-
-
Larson, S.B.1
Lucas, R.W.2
Greenwood, A.3
McPherson, A.4
-
22
-
-
13844266309
-
Crystallographic structure of the T = 1 particle of brome mosaic virus
-
S.B. Larson, R.W. Lucas, and A. McPherson Crystallographic structure of the T = 1 particle of brome mosaic virus J. Mol. Biol. 346 2005 815 831
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 815-831
-
-
Larson, S.B.1
Lucas, R.W.2
McPherson, A.3
-
23
-
-
0141457290
-
Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus
-
T. Lin, J. Cavarelli, and J.E. Johnson Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus Virology 314 2003 26 33
-
(2003)
Virology
, vol.314
, pp. 26-33
-
-
Lin, T.1
Cavarelli, J.2
Johnson, J.E.3
-
24
-
-
0035422346
-
Crystallization of brome mosaic virus and T = 1 brome mosaic virus particles following a structural transition
-
R.W. Lucas, Y.G. Kuznetsov, S.B. Larson, and A. McPherson Crystallization of brome mosaic virus and T = 1 brome mosaic virus particles following a structural transition Virology 286 2001 290 303
-
(2001)
Virology
, vol.286
, pp. 290-303
-
-
Lucas, R.W.1
Kuznetsov, Y.G.2
Larson, S.B.3
McPherson, A.4
-
25
-
-
0000217485
-
Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations
-
A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, and S. Ha Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations FASEB J. 6 1992 A143
-
(1992)
FASEB J.
, vol.6
, pp. 143
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
26
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, and S. Ha All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
27
-
-
1842454635
-
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs
-
A.L. Perryman, J.H. Lin, and J.A. McCammon HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs Protein Sci. 13 2004 1108 1123
-
(2004)
Protein Sci.
, vol.13
, pp. 1108-1123
-
-
Perryman, A.L.1
Lin, J.H.2
McCammon, J.A.3
-
29
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, and K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 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
-
30
-
-
0028321481
-
Three-dimensional structure of baculovirus-expressed norwalk virus capsids
-
B.V.V. Prasad, R. Rothnagel, X. Jiang, and M.K. Estes Three-dimensional structure of baculovirus-expressed norwalk virus capsids J. Virol. 8 1994 5117 5125
-
(1994)
J. Virol.
, vol.8
, pp. 5117-5125
-
-
Prasad, B.V.V.1
Rothnagel, R.2
Jiang, X.3
Estes, M.K.4
-
31
-
-
14844300852
-
Maturation dynamics of bacteriophage hk97 capsid
-
A.J. Rader, D.H. Vlad, and I. Bahar Maturation dynamics of bacteriophage hk97 capsid Structure 13 2005 413 421
-
(2005)
Structure
, vol.13
, pp. 413-421
-
-
Rader, A.J.1
Vlad, D.H.2
Bahar, I.3
-
32
-
-
0031961961
-
Energetics of quasiequivalence: Computational analysis of protein-protein interactions in icosahedral viruses
-
V.S. Reddy, H.A. Giesing, R.T. Morton, A. Kumar, C.B. Post, C.L. Brooks III, and J.E. Johnson Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses Biophys. J. 74 1998 546 558
-
(1998)
Biophys. J.
, vol.74
, pp. 546-558
-
-
Reddy, V.S.1
Giesing, H.A.2
Morton, R.T.3
Kumar, A.4
Post, C.B.5
Brooks III, C.L.6
Johnson, J.E.7
-
33
-
-
0028847094
-
Characterization of deletion and frameshift mutants of satellite tobacco mosaic virus
-
G. Routh, J.A. Dodds, L. Fitzmaurice, and T.E. Mirkov Characterization of deletion and frameshift mutants of satellite tobacco mosaic virus Virology 212 1995 121 127
-
(1995)
Virology
, vol.212
, pp. 121-127
-
-
Routh, G.1
Dodds, J.A.2
Fitzmaurice, L.3
Mirkov, T.E.4
-
34
-
-
0002373738
-
Algorithmic challenges in computational molecular biophysics
-
T. Schlick, R. Skeel, A. Brünger, L. Kalé, J.A. Board Jr., J. Hermans, and K. Schulten Algorithmic challenges in computational molecular biophysics J. Comput. Phys. 151 1999 9 48
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 9-48
-
-
Schlick, T.1
Skeel, R.2
Brünger, A.3
Kalé, L.4
Board Jr., J.A.5
Hermans, J.6
Schulten, K.7
-
35
-
-
0035138090
-
Molecular dynamics simulations of human rhinovirus and an antiviral compound
-
B. Speelman, B.R. Brooks, and C.B. Post Molecular dynamics simulations of human rhinovirus and an antiviral compound Biophys. J. 80 2001 121 129
-
(2001)
Biophys. J.
, vol.80
, pp. 121-129
-
-
Speelman, B.1
Brooks, B.R.2
Post, C.B.3
-
36
-
-
4444319422
-
Natural nanochemical building blocks: Icosahedral virus particles organized by attached oligonucleotides
-
E. Strable, J.E. Johnson, and M.G. Finn Natural nanochemical building blocks: icosahedral virus particles organized by attached oligonucleotides Nano Lett. 4 2004 1385 1389
-
(2004)
Nano Lett.
, vol.4
, pp. 1385-1389
-
-
Strable, E.1
Johnson, J.E.2
Finn, M.G.3
-
37
-
-
9644266693
-
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
-
F. Tama, and C.L. Brooks III Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis J. Mol. Biol. 345 2005 299 314
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 299-314
-
-
Tama, F.1
Brooks III, C.L.2
-
38
-
-
1642355235
-
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
-
F. Tama, O. Miyashita, and C.L. Brooks III Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis J. Mol. Biol. 337 2004 985 999
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 985-999
-
-
Tama, F.1
Miyashita, O.2
Brooks III, C.L.3
-
39
-
-
0035165261
-
The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA
-
L. Tang, K.N. Johnson, L.A. Ball, T. Lin, M. Yeager, and J.E. Johnson The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA Nat. Struct. Biol. 8 2001 77 83
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 77-83
-
-
Tang, L.1
Johnson, K.N.2
Ball, L.A.3
Lin, T.4
Yeager, M.5
Johnson, J.E.6
-
40
-
-
1542347791
-
Nodavirus coat protein imposes dodecahedral RNA structure independent of nucleotide sequence and length
-
M. Tihova, K.A. Dryden, T.L. Le, S.C. Harvey, J.E. Johnson, M. Yeager, and A. Schneemann Nodavirus coat protein imposes dodecahedral RNA structure independent of nucleotide sequence and length J. Virol. 78 2004 2897 2905
-
(2004)
J. Virol.
, vol.78
, pp. 2897-2905
-
-
Tihova, M.1
Dryden, K.A.2
Le, T.L.3
Harvey, S.C.4
Johnson, J.E.5
Yeager, M.6
Schneemann, A.7
-
41
-
-
0004918770
-
Interactions between satellite tobacco mosaic virus, helper tobamoviruses, and their hosts
-
R.A. Valverde, J.A. Heick, and J.A. Dodds Interactions between satellite tobacco mosaic virus, helper tobamoviruses, and their hosts Phytopathology 81 1991 99 104
-
(1991)
Phytopathology
, vol.81
, pp. 99-104
-
-
Valverde, R.A.1
Heick, J.A.2
Dodds, J.A.3
-
42
-
-
0027431751
-
The canine parvovirus empty capsid structure
-
H. Wu, and M.G. Rossmann The canine parvovirus empty capsid structure J. Mol. Biol. 233 1993 231 244
-
(1993)
J. Mol. Biol.
, vol.233
, pp. 231-244
-
-
Wu, H.1
Rossmann, M.G.2
-
43
-
-
7544243334
-
Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarsegrain RNA model and a monte carlo approach
-
D. Zhang, R. Konecny, N.A. Baker, and J.A. McCammon Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarsegrain RNA model and a monte carlo approach Biopolymers 75 2004 325 337
-
(2004)
Biopolymers
, vol.75
, pp. 325-337
-
-
Zhang, D.1
Konecny, R.2
Baker, N.A.3
McCammon, J.A.4
|