-
1
-
-
0002336164
-
Ring closure and local conformational deformations of chain molecules
-
N. Go and H. Scherage, Ring closure and local conformational deformations of chain molecules, Macromolecules 3(1970), pp. 178-187.
-
(1970)
Macromolecules
, vol.3
, pp. 178-187
-
-
Go, N.1
Scherage, H.2
-
2
-
-
0021403515
-
Monte-Carlo study on local and small-amplitude conformational fluctuation in hen egg-white lysozyme
-
H. Wakana, H. Wako, and N. Saito, Monte-Carlo study on local and small-amplitude conformational fluctuation in hen egg-white lysozyme, Int. J. Pept. Protein Res. 23(1984), pp. 315-323.
-
(1984)
Int. J. Pept. Protein Res.
, vol.23
, pp. 315-323
-
-
Wakana, H.1
Wako, H.2
Saito, N.3
-
3
-
-
84986531925
-
Long-time dynamics of a polymer with rigid body monomer units relating to a protein model - Comparison with the rouse model
-
E. W. Knapp, Long-time dynamics of a polymer with rigid body monomer units relating to a protein model - comparison with the rouse model, J. Comput. Chem. 13(1992), pp. 793-798.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 793-798
-
-
Knapp, E.W.1
-
4
-
-
78751661892
-
A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses
-
L. R. Dodd, T. D. Boone, and D. N. Theodorou, A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses, Mol. Phys. 78(1993), pp. 961-996.
-
(1993)
Mol. Phys.
, vol.78
, pp. 961-996
-
-
Dodd, L.R.1
Boone, T.D.2
Theodorou, D.N.3
-
5
-
-
0012312267
-
Off-lattice Monte-Carlo method with constraints - Long-time dynamics of a protein model without nonbonded interactions
-
E. W. Knapp and A. Irgensdefregger, Off-lattice Monte-Carlo method with constraints - Long-time dynamics of a protein model without nonbonded interactions, J. Comput. Chem. 14(1993), pp. 19-29.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 19-29
-
-
Knapp, E.W.1
Irgensdefregger, A.2
-
6
-
-
1442281405
-
A kinematic view of loop closure
-
E. A. Coutsias, C. Seok, M. P. Jacobson, and K. A. Dill, A kinematic view of loop closure, J. Comput. Chem. 25(2004), pp. 510-528.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 510-528
-
-
Coutsias, E.A.1
Seok, C.2
Jacobson, M.P.3
Dill, K.A.4
-
7
-
-
0001720782
-
Chain closure with bond angle variations
-
R. E. Bruccoleri and M. Karplus, Chain closure with bond angle variations, Macromolecules 18(1985), pp. 2767-2773.
-
(1985)
Macromolecules
, vol.18
, pp. 2767-2773
-
-
Bruccoleri, R.E.1
Karplus, M.2
-
8
-
-
0012289137
-
An energy function for dynamics simulations of polypeptides in torsion angle space
-
F. Sartori, B. Melchers, H. Bottcher, and E. W. Knapp, An energy function for dynamics simulations of polypeptides in torsion angle space, J. Chem. Phys. 108(1998), pp. 8264-8276. (Pubitemid 128598549)
-
(1998)
Journal of Chemical Physics
, vol.108
, Issue.19
, pp. 8264-8276
-
-
Sartori, F.1
Melchers, B.2
Bottcher, H.3
Knapp, E.W.4
-
9
-
-
0000643670
-
A configurational bias Monte Carlo method for linear and cyclic peptides
-
M. W. Deem and J. S. Bader, A configurational bias Monte Carlo method for linear and cyclic peptides, Mol. Phys. 87(1996), pp. 1245-1260. (Pubitemid 126467110)
-
(1996)
Molecular Physics
, vol.87
, Issue.6
, pp. 1245-1260
-
-
Deem, M.W.1
Bader, J.S.2
-
10
-
-
0001098882
-
Local deformations of polymers with nonplanar rigid main-chain internal coordinates
-
A. R. Dinner, Local deformations of polymers with nonplanar rigid main-chain internal coordinates, J. Comput. Chem. 21(2000), pp. 1132-1144.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1132-1144
-
-
Dinner, A.R.1
-
11
-
-
0035826575
-
Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space
-
DOI 10.1063/1.1364637
-
G. Favrin, A. Irback, and F. Sjunnesson, Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space, J. Chem. Phys. 114(2001), pp. 8154-8158. (Pubitemid 32486731)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.18
, pp. 8154-8158
-
-
Favrin, G.1
Irback, A.2
Sjunnesson, F.3
-
12
-
-
0037337891
-
Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias
-
J. P. Ulmschneider and W. L. Jorgensen, Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias, J. Chem. Phys. 118(2003), pp. 4261-4271.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 4261-4271
-
-
Ulmschneider, J.P.1
Jorgensen, W.L.2
-
13
-
-
1242314248
-
Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation
-
J. P. Ulmschneider and W. L. Jorgensen, Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation, J. Am. Chem. Soc. 126(2004), pp. 1849-1857. (Pubitemid 38222770)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.6
, pp. 1849-1857
-
-
Ulmschneider, J.P.1
Jorgensen, W.L.2
-
14
-
-
8344258212
-
Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles
-
J. O. Ulmschneider and W. L. Jorgensen, Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles, J. Phys. Chem. B 108(2004), pp. 16883-16892.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 16883-16892
-
-
Ulmschneider, J.O.1
Jorgensen, W.L.2
-
15
-
-
33748574268
-
Monte carlo vs molecular dynamics for all-atom polypeptide folding simulations
-
DOI 10.1021/jp061619b
-
J. P. Ulmschneider, M. B. Ulmschneider, and A. Di Nola, Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations, J. Phys. Chem. B 110(2006), pp. 16733-16742. (Pubitemid 44373403)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.33
, pp. 16733-16742
-
-
Ulmschneider, J.P.1
Ulmschneider, M.B.2
De Nola, A.3
-
16
-
-
79958847459
-
RNA conformational sampling: II. Arbitrary-length multi-nucleotide loop closure
-
in press
-
C. H. Mak, W.-Y. Chung, and N. D. Markivskiy, RNA conformational sampling: II. Arbitrary-length multi-nucleotide loop closure, J. Chem. Theo. Comput. (2010), in press.
-
(2010)
J. Chem. Theo. Comput.
-
-
Mak, C.H.1
Chung, W.-Y.2
Markivskiy, N.D.3
-
17
-
-
41549169141
-
RNA conformational sampling. I. Single-nucleotide loop closure
-
DOI 10.1002/jcc.20851
-
C. H. Mak, RNA conformational sampling: 1. Single-nucleotide loop closure, J. Comput. Chem. 29(2008), pp. 926-933. (Pubitemid 351473689)
-
(2008)
Journal of Computational Chemistry
, vol.29
, Issue.6
, pp. 926-933
-
-
Mak, C.H.1
-
18
-
-
0000781576
-
Exact analytical loop closure in proteins using polynomial equations
-
W. J. Wedemeyer and H. A. Scheraga, Exact analytical loop closure in proteins using polynomial equations, J. Comput. Chem. 20(1999), pp. 819-844. (Pubitemid 129656130)
-
(1999)
Journal of Computational Chemistry
, vol.20
, Issue.8
, pp. 819-844
-
-
Wedemeyer, W.J.1
Scheraga, H.A.2
-
21
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
P. J. Kraulis, MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24(1991), pp. 946-950.
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
22
-
-
17444371974
-
Mobility analysis of RSSR mechanisms by working volume
-
W. Y. Chung, Mobility analysis of RSSR mechanisms by working volume, Trans. ASME 127(2005), pp. 156-159.
-
(2005)
Trans. ASME
, vol.127
, pp. 156-159
-
-
Chung, W.Y.1
-
23
-
-
0003600912
-
-
Academic Press, San Diego, CA
-
A. S. Glassner, Graphics Gems, Academic Press, San Diego, CA, 1990.
-
(1990)
Graphics Gems
-
-
Glassner, A.S.1
-
24
-
-
0004161838
-
-
New York, Cambridge
-
W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling, Numerical Recipes, New York, Cambridge, 1992.
-
(1992)
Numerical Recipes
-
-
Press, W.H.1
Flannery, B.P.2
Teukolsky, S.A.3
Vetterling, W.T.4
-
25
-
-
84988112508
-
An efficient Newton-like method for molecular mechanics energy minimization of large molecules
-
J. W. Ponder and F. M. Richards, An efficient Newton-like method for molecular mechanics energy minimization of large molecules, J. Comput. Chem. 8(1987), pp. 1016-1024.
-
(1987)
J. Comput. Chem.
, vol.8
, pp. 1016-1024
-
-
Ponder, J.W.1
Richards, F.M.2
-
27
-
-
0023663396
-
Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites
-
A. C. Forster and R. H. Symons, Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites, Cell 49(1987), pp. 211-220.
-
(1987)
Cell.
, vol.49
, pp. 211-220
-
-
Forster, A.C.1
Symons, R.H.2
-
28
-
-
0028063567
-
3-dimensional structure of a hammerhead ribozyme
-
H. W. Pley, K. M. Flaherty, and D. B. McKay, 3-dimensional structure of a hammerhead ribozyme, Nature 372(1994), pp. 68-74.
-
(1994)
Nature
, vol.372
, pp. 68-74
-
-
Pley, H.W.1
Flaherty, K.M.2
McKay, D.B.3
-
29
-
-
0029073091
-
The crystal structure of an all-RNA hammerhead ribozyme - A proposed mechanism for RNA catalytic cleavage
-
W. G. Scott, J. T. Finch, and A. Klug, The crystal structure of an all-RNA hammerhead ribozyme - a proposed mechanism for RNA catalytic cleavage, Cell 81(1995), pp. 991-1002.
-
(1995)
Cell.
, vol.81
, pp. 991-1002
-
-
Scott, W.G.1
Finch, J.T.2
Klug, A.3
-
30
-
-
41749101497
-
-
D. M. J. Lilley and F. Eckstein, eds., Royal Society of Chemistry, London
-
D. Lambert and J. M. Burke, Ribozymes and RNA Catalysis, D. M. J. Lilley and F. Eckstein, eds., Royal Society of Chemistry, London, 2008.
-
(2008)
Ribozymes and RNA Catalysis
-
-
Lambert, D.1
Burke, J.M.2
-
31
-
-
41749101497
-
-
M. J. Lilley and F. Eckstein, eds., Royal Society of Chemistry, London
-
W. G. Scott, in Ribozymes and RNA Catalysis, M. J. Lilley and F. Eckstein, eds., Royal Society of Chemistry, London, 2008.
-
(2008)
Ribozymes and RNA Catalysis
-
-
Scott, W.G.1
-
34
-
-
41749101497
-
-
M. J. Lilley, and F. Eckstein, eds., Royal Society of Chemistry, London
-
S. A. Woodson and P. Rangan, Ribozymes and RNA Catalysis, M. J. Lilley, and F. Eckstein, eds., Royal Society of Chemistry, London, 2008.
-
(2008)
Ribozymes and RNA Catalysis
-
-
Woodson, S.A.1
Rangan, P.2
-
35
-
-
33746228126
-
Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis
-
DOI 10.1016/j.cell.2006.06.036, PII S0092867406008567
-
M. Martick and W. G. Scott, Tertiary contacts distant from the active site prime a ribozyme for catalysis, Cell 126(2006), pp. 309-320. (Pubitemid 44092962)
-
(2006)
Cell
, vol.126
, Issue.2
, pp. 309-320
-
-
Martick, M.1
Scott, W.G.2
-
36
-
-
0029878720
-
VMD - Visual molecular dynamics
-
W. Humphrey, A. Dalke, and K. Schulten, VMD - visual molecular dynamics, J. Mol. Graph. 14(1996), pp. 33-38.
-
(1996)
J. Mol. Graph
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
37
-
-
1942533453
-
Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements
-
DOI 10.1261/rna.5268404
-
J. C. Penedo, T. J. Wilson, S. D. Jayasena, A. Khvorova, and D. M. Lilley, Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements, RNA 10(2004), pp. 880-888. (Pubitemid 38529750)
-
(2004)
RNA
, vol.10
, Issue.5
, pp. 880-888
-
-
Penedo, J.C.1
Wilson, T.J.2
Jayasena, S.D.3
Khvorova, A.4
Lilley, D.M.J.5
-
38
-
-
0034743153
-
Early events in RNA folding
-
D. Thirumalai, N. Lee, S. A. Woodson, and D. K. Klimov, Early events in RNA folding, Annu. Rev. Phys. Chem. 52(2001), pp. 751-761.
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 751-761
-
-
Thirumalai, D.1
Lee, N.2
Woodson, S.A.3
Klimov, D.K.4
-
40
-
-
0032922174
-
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
-
T. E. Cheatham III, P. Cieplak, and P. A. Kollman, A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat, J. Biomol. Struct. Dyn. 16(1999), pp. 845-862. (Pubitemid 29157655)
-
(1999)
Journal of Biomolecular Structure and Dynamics
, vol.16
, Issue.4
, pp. 845-862
-
-
Cheatham III, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
41
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
D. Qiu, P. S. Shenkin, F. P. Hollinger, and W. C. Still, The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate radii, J. Phys. Chem. A 101(1997), pp. 3005-3014. (Pubitemid 127580882)
-
(1997)
Journal of Physical Chemistry A
, vol.101
, Issue.16
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
42
-
-
0036903567
-
Folding and activity of the hammerhead ribozyme
-
DOI 10.1002/1439-7633(20020802) 3:8<690::AID-CBIC690>3.0.CO;2-C
-
C. Hammann and D. M. Lilley, Folding and activity of the hammerhead ribozyme, Chembiochem 3(2002), pp. 690-700. (Pubitemid 36004508)
-
(2002)
ChemBioChem
, vol.3
, Issue.8
, pp. 690-700
-
-
Hammann, C.1
Lilley, D.M.J.2
-
43
-
-
0031463467
-
Ion-induced folding of the hammerhead ribozyme: A fluorescence resonance energy transfer study
-
DOI 10.1093/emboj/16.24.7481
-
G. S. Bassi, A. I. Murchie, F. Walter, R. M. Clegg, and D. M. Lilley, Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study, EMBO J. 16(1997), pp. 7481-7489. (Pubitemid 28010507)
-
(1997)
EMBO Journal
, vol.16
, Issue.24
, pp. 7481-7489
-
-
Bassi, G.S.1
Murchie, A.I.H.2
Walter, F.3
Clegg, R.M.4
Lilley, D.M.J.5
|