-
2
-
-
84986512474
-
CHARMM: A program for energy, minimization, and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: A program for energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187.
-
(1983)
J. Comp. Chem.
, vol.4
, pp. 187
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
3
-
-
0019387686
-
Structure of a B-DNA dodecamer. II. Influence of hase sequence on helix structure
-
Dickerson, R. E. and H. R. Drew. 1981. Structure of a B-DNA dodecamer. II. Influence of hase sequence on helix structure. J. Mol. Biol. 149: 761-786.
-
(1981)
J. Mol. Biol.
, vol.149
, pp. 761-786
-
-
Dickerson, R.E.1
Drew, H.R.2
-
4
-
-
0027510086
-
A Monte-Carlo method for generating structures of short-stranded DNA sequences
-
and supplemental material available from journal
-
Erie, D. A., K. J. Breslauer, and W. K. Olson. 1993. A Monte-Carlo method for generating structures of short-stranded DNA sequences. Biopolymers. 33:75-105 (and supplemental material available from journal).
-
(1993)
Biopolymers
, vol.33
, pp. 75-105
-
-
Erie, D.A.1
Breslauer, K.J.2
Olson, W.K.3
-
5
-
-
0000615669
-
Function minimization by conjugate gradients
-
Fletcher, R., and C. M. Reeves. 1964. Function minimization by conjugate gradients. Comput. J. 7:149.
-
(1964)
Comput. J.
, vol.7
, pp. 149
-
-
Fletcher, R.1
Reeves, C.M.2
-
7
-
-
0026816545
-
The electrostatic contribution to DNA base-stacking interactions
-
Friedman, R. A., and B. Honig. 1992. The electrostatic contribution to DNA base-stacking interactions. Biopolymers. 32:144-159.
-
(1992)
Biopolymers
, vol.32
, pp. 144-159
-
-
Friedman, R.A.1
Honig, B.2
-
8
-
-
0001199024
-
Conformational transitions in potential and free energy space for furanoses and 2′-deoxynucleosides
-
Gabb, H. A., and S. Harvey. 1993. Conformational transitions in potential and free energy space for furanoses and 2′-deoxynucleosides. J. Am. Chem. Soc. 115:4218-4227.
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 4218-4227
-
-
Gabb, H.A.1
Harvey, S.2
-
9
-
-
0021097106
-
The combinatorial distance geometry method for the calculation of molecular conformation. II. Sample problems and computational statistics
-
Havel, T. F., G. M. Crippen, I. D. Kuntz, and J. M. Blaney. 1983a. The combinatorial distance geometry method for the calculation of molecular conformation. II. Sample problems and computational statistics. J. Theor. Biol. 104:383-400.
-
(1983)
J. Theor. Biol.
, vol.104
, pp. 383-400
-
-
Havel, T.F.1
Crippen, G.M.2
Kuntz, I.D.3
Blaney, J.M.4
-
10
-
-
0021097083
-
The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem
-
Havel, T. F., I. D. Kuntz, and G. M. Crippen. 1983b. The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem. J. Theor. Biol. 104:359-381.
-
(1983)
J. Theor. Biol.
, vol.104
, pp. 359-381
-
-
Havel, T.F.1
Kuntz, I.D.2
Crippen, G.M.3
-
12
-
-
84990406847
-
Dielectric effects in biopolymers: The theory of ionic saturation revisited
-
Hingerty, B. E., R. H. Ritchie, T. L. Ferrell, and J. E. Turner. 1985. Dielectric effects in biopolymers: the theory of ionic saturation revisited. Biopolymers. 24:427-439.
-
(1985)
Biopolymers
, vol.24
, pp. 427-439
-
-
Hingerty, B.E.1
Ritchie, R.H.2
Ferrell, T.L.3
Turner, J.E.4
-
14
-
-
0026941316
-
Variable ranges of interactions in polypeptide conformations with a method to complement molecular modeling
-
Jacchieri, S., and R. L. Jernigan. 1992. Variable ranges of interactions in polypeptide conformations with a method to complement molecular modeling. Biopolymers. 32:1327-1388.
-
(1992)
Biopolymers
, vol.32
, pp. 1327-1388
-
-
Jacchieri, S.1
Jernigan, R.L.2
-
15
-
-
0024580271
-
The electrostatic potential of B-DNA
-
Jayaram, B., K. A. Sharp, and B. Honig. 1989. The electrostatic potential of B-DNA. Biopolymers. 28:975-993.
-
(1989)
Biopolymers
, vol.28
, pp. 975-993
-
-
Jayaram, B.1
Sharp, K.A.2
Honig, B.3
-
16
-
-
9544241009
-
-
Laboratorie de Biochimie Theorique CNRS, Institut de Biologie Physico-Chimique, Paris
-
Lavery, R. 1990. JUMNA IIIe. Laboratorie de Biochimie Theorique CNRS, Institut de Biologie Physico-Chimique, Paris.
-
(1990)
JUMNA IIIe
-
-
Lavery, R.1
-
17
-
-
0026253724
-
Distance-dependent dielectric constants and their application to double-helical DNA
-
Mazur, J., and R. L. Jernigan. 1991. Distance-dependent dielectric constants and their application to double-helical DNA. Biopolymers. 31: 1615-1629.
-
(1991)
Biopolymers
, vol.31
, pp. 1615-1629
-
-
Mazur, J.1
Jernigan, R.L.2
-
18
-
-
0028923794
-
Comparison of rotation models for describing DNA conformation: Application to static and polymorphic forms
-
Mazur, J., and R. L. Jernigan. 1995. Comparison of rotation models for describing DNA conformation: Application to static and polymorphic forms. Biophys. J. 68:1472-1489.
-
(1995)
Biophys. J.
, vol.68
, pp. 1472-1489
-
-
Mazur, J.1
Jernigan, R.L.2
-
19
-
-
0024360615
-
Sequence dependence of the B-A conformational transition of DNA
-
Mazur, J., A. Sarai, and R. L. Jernigan. 1989. Sequence dependence of the B-A conformational transition of DNA. Biopolymers. 28:1223-1233.
-
(1989)
Biopolymers
, vol.28
, pp. 1223-1233
-
-
Mazur, J.1
Sarai, A.2
Jernigan, R.L.3
-
21
-
-
0022419269
-
The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG)-poly(dC)
-
McCall, M., T. Brown, and O. Kennard. 1985. The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG)-poly(dC). J. Mol. Biol. 183:385-398.
-
(1985)
J. Mol. Biol.
, vol.183
, pp. 385-398
-
-
McCall, M.1
Brown, T.2
Kennard, O.3
-
23
-
-
0024287459
-
Three-dimensional structure of plastocyanin from the green alga Scenedesmus obliquus
-
Moore, J. M., D. A. Case, W. J. Chazin, G. P. Gippert, T. F. Havel, R. Powls, and P. E. Wright. 1988. Three-dimensional structure of plastocyanin from the green alga Scenedesmus obliquus. Science. 240: 314-317.
-
(1988)
Science
, vol.240
, pp. 314-317
-
-
Moore, J.M.1
Case, D.A.2
Chazin, W.J.3
Gippert, G.P.4
Havel, T.F.5
Powls, R.6
Wright, P.E.7
-
24
-
-
0019923858
-
How flexible is the furanose ring? 2. An updated potential energy estimate
-
Olson, W. K. 1982. How flexible is the furanose ring? 2. An updated potential energy estimate. J. Am. Chem. Soc. 104:278-286.
-
(1982)
J. Am. Chem. Soc.
, vol.104
, pp. 278-286
-
-
Olson, W.K.1
-
25
-
-
0022651289
-
Simulation of interactions between nucleic acid bases by refined atom-atom potential functions
-
Poltev, V. I., and N. V. Shulyupina. 1986. Simulation of interactions between nucleic acid bases by refined atom-atom potential functions. J. Biomol. Struct. Dyn. 3:739-765.
-
(1986)
J. Biomol. Struct. Dyn.
, vol.3
, pp. 739-765
-
-
Poltev, V.I.1
Shulyupina, N.V.2
-
26
-
-
0000777707
-
Energetics coupling between DNA bending and base pair opening
-
Ramstein, J., and R. Lavery. 1988. Energetics coupling between DNA bending and base pair opening. Proc. Natl. Acad. Sci. USA. 85: 7231-7235.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 7231-7235
-
-
Ramstein, J.1
Lavery, R.2
-
27
-
-
0017542708
-
Energetics of defect motion which transports polyethylene molecules along their axis
-
Reneker, D. H., B. M. Fanconi, and J. Mazur. 1977. Energetics of defect motion which transports polyethylene molecules along their axis. J. Appl. Phys. 48:4032-4042.
-
(1977)
J. Appl. Phys.
, vol.48
, pp. 4032-4042
-
-
Reneker, D.H.1
Fanconi, B.M.2
Mazur, J.3
-
28
-
-
0023844376
-
Small defects in crystalline polyethylene
-
Reneker, D. H., and J. Mazur. 1987. Small defects in crystalline polyethylene. Polymer. 29:3-14.
-
(1987)
Polymer
, vol.29
, pp. 3-14
-
-
Reneker, D.H.1
Mazur, J.2
-
29
-
-
0015004691
-
Stereochemistry of nucleic acids and polynucleotides. III. Electronic charge distribution
-
Renugopalakrisnan, V. A., V. Lakshminarayana, and V. Sasisekharan. 1971. Stereochemistry of nucleic acids and polynucleotides. III. Electronic charge distribution. Biopolymers. 10:1159-1167.
-
(1971)
Biopolymers
, vol.10
, pp. 1159-1167
-
-
Renugopalakrisnan, V.A.1
Lakshminarayana, V.2
Sasisekharan, V.3
-
30
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., G. Ciccoti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327.
-
(1977)
J. Comp. Phys.
, vol.23
, pp. 327
-
-
Ryckaert, J.P.1
Ciccoti, G.2
Berendsen, H.J.C.3
-
32
-
-
1642441281
-
Sequence dependence of DNA conformations: Means and fluctuations
-
W. K. Olson, M. H. Sarma, and M. Sundaralingam, editors. Adenine Press, Schenectady, New York
-
Sarai, A., J. Mazur, R. Nussinov, and R. L. Jernigan. 1988. Sequence dependence of DNA conformations: means and fluctuations. In Structure and Expressions, Vol. 3. W. K. Olson, M. H. Sarma, and M. Sundaralingam, editors. Adenine Press, Schenectady, New York. 213-223.
-
(1988)
Structure and Expressions
, vol.3
, pp. 213-223
-
-
Sarai, A.1
Mazur, J.2
Nussinov, R.3
Jernigan, R.L.4
-
33
-
-
0023350241
-
Nucleic acid model building: The multiple backbone solutions associated with a given base morphology
-
Srinivasan, A. R., and W. K. Olson. 1987. Nucleic acid model building: the multiple backbone solutions associated with a given base morphology. J. Biomol. Struct. Dyn. 4:895-938.
-
(1987)
J. Biomol. Struct. Dyn.
, vol.4
, pp. 895-938
-
-
Srinivasan, A.R.1
Olson, W.K.2
-
34
-
-
33845554708
-
Crystallographic evidence for the existence of C-H-O, C-H-N, and C-H-Cl hydrogen bonds
-
Taylor, R., and O. Kennard. 1982. Crystallographic evidence for the existence of C-H-O, C-H-N, and C-H-Cl hydrogen bonds. J. Am. Chem. Soc. 104:5063-5070.
-
(1982)
J. Am. Chem. Soc.
, vol.104
, pp. 5063-5070
-
-
Taylor, R.1
Kennard, O.2
-
35
-
-
0026683994
-
A reduced set of coordinates for modeling DNA structures: (I) B-to-A transition pathway driven by pseudorotation angle
-
Tung, C.-S. 1992. A reduced set of coordinates for modeling DNA structures: (I) B-to-A transition pathway driven by pseudorotation angle. J. Biomol. Struct. Dyn. 9:1185-1194.
-
(1992)
J. Biomol. Struct. Dyn.
, vol.9
, pp. 1185-1194
-
-
Tung, C.-S.1
-
36
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner, S. J., P. A. Kollman, D. A. Case, J. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. J. Weiner. 1984. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, J.C.4
Ghio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.J.8
-
37
-
-
0028950075
-
Forces of tertiary structural organization of globular proteins
-
Yue, K., and K. A. Dill. 1995. Forces of tertiary structural organization of globular proteins. Proc. Natl. Acad. Sci. USA. 92:146-150.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 146-150
-
-
Yue, K.1
Dill, K.A.2
-
38
-
-
0028295631
-
Multiple copy sampling in protein loop modeling: Computational efficiency and sensitivity to dihedral angle perturbations
-
Zheng, Q., R. Rosenfeld, C. DeLisi, and D. J. Kyle. 1994. Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations. Protein Sci. 3:493-506.
-
(1994)
Protein Sci.
, vol.3
, pp. 493-506
-
-
Zheng, Q.1
Rosenfeld, R.2
DeLisi, C.3
Kyle, D.J.4
-
39
-
-
0001894605
-
Loop closure via bond scaling and relaxation
-
Zheng, Q., R. Rosenfeld, S. Vaida, and C. Delisi. 1993a. Loop closure via bond scaling and relaxation. J. Comp. Chem. 14:556-565.
-
(1993)
J. Comp. Chem.
, vol.14
, pp. 556-565
-
-
Zheng, Q.1
Rosenfeld, R.2
Vaida, S.3
DeLisi, C.4
-
40
-
-
0027164958
-
Determining protein loop conformation using scaling-relaxation techniques
-
Zheng, Q., R. Rosenfeld, S. Vaida, and C. Delisi. 1993b. Determining protein loop conformation using scaling-relaxation techniques. Protein Sci. 2:1242-1248.
-
(1993)
Protein Sci.
, vol.2
, pp. 1242-1248
-
-
Zheng, Q.1
Rosenfeld, R.2
Vaida, S.3
DeLisi, C.4
-
41
-
-
0000114860
-
Atom-atom potential functions for conformational calculations of nucleic acids
-
Zhurkin, V. B., V. I. Poltev, and V. I. Florent'ev. 1981. Atom-atom potential functions for conformational calculations of nucleic acids. Mol. Biol. 14:887-895.
-
(1981)
Mol. Biol.
, vol.14
, pp. 887-895
-
-
Zhurkin, V.B.1
Poltev, V.I.2
Florent'ev, V.I.3
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