-
1
-
-
0029920331
-
Specificity of ribonucleoprotein interaction detennined by RNA folding during complex formation
-
Allain, F. H.-T., C. C. Gubser, P. W. A. Howe, K. Nagai, D. Neuhaus, and G. Varani. 1996. Specificity of ribonucleoprotein interaction detennined by RNA folding during complex formation. Nature. 380:646-650.
-
(1996)
Nature.
, vol.380
, pp. 646-650
-
-
Allain, F.H.-T.1
Gubser, C.C.2
Howe, P.W.A.3
Nagai, K.4
Neuhaus, D.5
Varani, G.6
-
2
-
-
0030755124
-
Structural basis of the RNA-binding specificity of human U1A protein
-
Allain, F. H.-T., P. W. A. Howe, D. Neuhaus, and G. Varani. 1997. Structural basis of the RNA-binding specificity of human U1A protein. EMBO J. 16:5764-5774.
-
(1997)
EMBO J.
, vol.16
, pp. 5764-5774
-
-
Allain, F.H.-T.1
Howe, P.W.A.2
Neuhaus, D.3
Varani, G.4
-
3
-
-
0030813208
-
Structures of RNA-binding proteins
-
Amez, J. G., and J. Cavarelli. 1997. Structures of RNA-binding proteins. Q. Rev. Biophys. 30:195-240.
-
(1997)
Q. Rev. Biophys.
, vol.30
, pp. 195-240
-
-
Amez, J.G.1
Cavarelli, J.2
-
4
-
-
0032907143
-
Molecular dynamics simulations of solvated yeast tRNAAsp
-
Auffinger, P., S. Louise-May, and E. Westhof. 1999. Molecular dynamics simulations of solvated yeast tRNAAsp. Biophys. J. 76:50-64.
-
(1999)
Biophys. J.
, vol.76
, pp. 50-64
-
-
Auffinger, P.1
Louise-May, S.2
Westhof, E.3
-
5
-
-
0031566427
-
RNA hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated tRNAAsp anticodon hairpin
-
Auffinger, P., and E. Westhof. 1997. RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNAAsp anticodon hairpin. J. Mol. Biol. 269:326-341.
-
(1997)
J. Mol. Biol.
, vol.269
, pp. 326-341
-
-
Auffinger, P.1
Westhof, E.2
-
6
-
-
0032054952
-
Simulations of the molecular dynamics of nucleic acids
-
Auffinger, P., and E. Westhof. 1998. Simulations of the molecular dynamics of nucleic acids. Curr. Opin. Struct. Biol. 8:227-236.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 227-236
-
-
Auffinger, P.1
Westhof, E.2
-
7
-
-
33847526306
-
-
Avis, J. M., F. H.-T. Allain, P. W. A. Howe, G. Varani, K. Nagai, and D. Neuhaus. 1996. Solution structure of the N-terminal RNP domain of
-
(1996)
Solution Structure of the N-terminal RNP Domain of
-
-
Avis, J.M.1
Allain, F.H.-T.2
Howe, P.W.A.3
Varani, G.4
Nagai, K.5
Neuhaus, D.6
-
8
-
-
0029978824
-
U1A protein: The role of C-terminal residues in structure stability and RNA binding
-
U1A protein: the role of C-terminal residues in structure stability and RNA binding. J. Mol. Biol. 257:398-411.
-
J. Mol. Biol.
, vol.257
, pp. 398-411
-
-
-
9
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
10
-
-
0017411710
-
The Protein Data Bank
-
Bernstein, F. C., T. F. Koetzle, G. J. B. Willians, E. F. Mayer, J. M. D. Brice, J. R. Rodgers, Q. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The Protein Data Bank. A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
-
(1977)
A Computer-based Archival File for Macromolecular Structures. J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Willians, G.J.B.3
Mayer, E.F.4
Brice, J.M.D.5
Rodgers, J.R.6
Kennard, Q.7
Shimanouchi, T.8
Tasumi, M.9
-
11
-
-
0027471377
-
The human U1 snRNP-specific U1A protein inhibits polyadenylation of its own pre-mRNA
-
Boelens, W.-C., E. J. Jansen, W. J. van Venrooij, R. Stripecke, I. W. Mattaj, and S. I. Gunderson. 1993. The human U1 snRNP-specific U1A protein inhibits polyadenylation of its own pre-mRNA. Cell. 72:881-892.
-
(1993)
Cell.
, vol.72
, pp. 881-892
-
-
Boelens, W.-C.1
Jansen, E.J.2
Van Venrooij, W.J.3
Stripecke, R.4
Mattaj, I.W.5
Gunderson, S.I.6
-
12
-
-
84986512474
-
CHARMM: A program for macromolecular 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 macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
13
-
-
0024250301
-
Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
-
Brünger, A., and M. Karplus. 1988. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins. 4:148-156.
-
(1988)
Proteins.
, vol.4
, pp. 148-156
-
-
Brünger, A.1
Karplus, M.2
-
14
-
-
0028129989
-
Conserved structures and diversity of functions of RNA-binding proteins
-
Burd, C. G., and G. Dreyfuss. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science. 265:615-621.
-
(1994)
Science.
, vol.265
, pp. 615-621
-
-
Burd, C.G.1
Dreyfuss, G.2
-
15
-
-
0001122076
-
Simulation of a protein crystal at constant pressure
-
Ceccarelli, M., and M. Marchi. 1997. Simulation of a protein crystal at constant pressure. J. Phys. Chem. B. 101:2105-2108.
-
(1997)
J. Phys. Chem. B.
, vol.101
, pp. 2105-2108
-
-
Ceccarelli, M.1
Marchi, M.2
-
16
-
-
0030953141
-
Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes
-
Cheatham, T. E., Ill, and P. A. Kollman. 1997. Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119: 4805-4825.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 4805-4825
-
-
Cheatham Ill, T.E.1
Kollman, P.A.2
-
17
-
-
0029071516
-
Protein-RNA recognition
-
Draper, D. E. 1995. Protein-RNA recognition. Annu. Rev. Biochem. 64: 593-620.
-
(1995)
Annu. Rev. Biochem.
, vol.64
, pp. 593-620
-
-
Draper, D.E.1
-
18
-
-
0028814905
-
Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution
-
Eriksson, M. A. L., T. Hard, and L. Nilsson. 1995. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophys. J. 68:402-426.
-
(1995)
Biophys. J.
, vol.68
, pp. 402-426
-
-
Eriksson, M.A.L.1
Hard, T.2
Nilsson, L.3
-
19
-
-
0032559232
-
Induced folding in RNA-protein recognition: More than a simple molecular handshake
-
Frankel, A. D., and C. A. Smith. 1998. Induced folding in RNA-protein recognition: more than a simple molecular handshake. Cell. 92: 149-151.
-
(1998)
Cell.
, vol.92
, pp. 149-151
-
-
Frankel, A.D.1
Smith, C.A.2
-
20
-
-
0030069826
-
Structure of the polyadenylation regulatory element of the human U1A pre-mRNA 3′-untranslated region and interaction with the U1A protein
-
Gubser, C. C., and G. Varani. 1996. Structure of the polyadenylation regulatory element of the human U1A pre-mRNA 3′-untranslated region and interaction with the U1A protein. Biochemistry. 35:2253-2267.
-
(1996)
Biochemistry.
, vol.35
, pp. 2253-2267
-
-
Gubser, C.C.1
Varani, G.2
-
21
-
-
0027956671
-
Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain
-
Hall, K. B. 1994. Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain. Biochemistry. 33:10076-10088.
-
(1994)
Biochemistry.
, vol.33
, pp. 10076-10088
-
-
Hall, K.B.1
-
22
-
-
0031915278
-
Molecular dynamics investigations of hammerhead ribozyme RNA
-
Hermann, T., P. Auffinger, and E. Westhof. 1998. Molecular dynamics investigations of hammerhead ribozyme RNA. Eur. Biophys. J. 27: 153-165.
-
(1998)
Eur. Biophys. J.
, vol.27
, pp. 153-165
-
-
Hermann, T.1
Auffinger, P.2
Westhof, E.3
-
24
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 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
-
25
-
-
0030585191
-
Two structurally different RNA molecules are bound by the spliceosomal protein U1A using the same recognition strategy
-
Jovine, L., C. Oubridge, J. M. Avis, and K. Nagai. 1996. Two structurally different RNA molecules are bound by the spliceosomal protein U1A using the same recognition strategy. Structure. 4:621-631.
-
(1996)
Structure.
, vol.4
, pp. 621-631
-
-
Jovine, L.1
Oubridge, C.2
Avis, J.M.3
Nagai, K.4
-
26
-
-
0025048105
-
Molecular dynamics simulations in biology
-
Karplus, M., and G. A. Petsko. 1990. Molecular dynamics simulations in biology. Nature. 347:631-639.
-
(1990)
Nature.
, vol.347
, pp. 631-639
-
-
Karplus, M.1
Petsko, G.A.2
-
27
-
-
0026785575
-
Molecular dynamics simulation of solvated protein at high pressure
-
Kitchen, D. B., L. H. Reed, and R. M. Levy. 1992. Molecular dynamics simulation of solvated protein at high pressure. Biochemistry. 31: 10083-10093.
-
(1992)
Biochemistry.
, vol.31
, pp. 10083-10093
-
-
Kitchen, D.B.1
Reed, L.H.2
Levy, R.M.3
-
28
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
29
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
30
-
-
0028965970
-
An RED that does not bind RNA: NMR secondary structure determination and biochemical properties of the C-terminal RNA binding domain from the human U1A protein
-
Lu, J., and K. B. Hall. 1995. An RED that does not bind RNA: NMR secondary structure determination and biochemical properties of the C-terminal RNA binding domain from the human U1A protein. J. Mol. Biol. 247:739-752.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 739-752
-
-
Lu, J.1
Hall, K.B.2
-
31
-
-
0025173604
-
Structure of spliceosomal snRNPs and their role in pre-mRNA splicing
-
Lührmann, R., B. Kastner, and M. Bach. 1990. Structure of spliceosomal snRNPs and their role in pre-mRNA splicing. Biochim. Biophys. Acta. 1087:265-292.
-
(1990)
Biochim. Biophys. Acta.
, vol.1087
, pp. 265-292
-
-
Lührmann, R.1
Kastner, B.2
Bach, M.3
-
32
-
-
0025127420
-
Quantitative determination that one of two potential RNA-binding domains of the a protein component of the U1 small nuclear ribonucleoprotein complex binds with high affinity to stem-loop II of Ul RNA
-
Lutz-Freyermuth, C.t C. C. Query, and J. D. Keene. 1990. Quantitative determination that one of two potential RNA-binding domains of the A protein component of the U1 small nuclear ribonucleoprotein complex binds with high affinity to stem-loop II of Ul RNA. Proc. Natl. Acad. Sci. USA. 87:6393-6397.
-
(1990)
Proc. Natl. Acad. Sci. USA.
, vol.87
, pp. 6393-6397
-
-
Lutz-Freyermuth1
Query, C.C.C.2
Keene, J.D.3
-
33
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stole, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
-
(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.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stole, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
34
-
-
6344260593
-
An all-atom empirical energy function for the simulation of nucleic acids
-
MacKerell, A. D., Jr., J. Wiorkiewicz-Kuczera, and M. Karplus. 1995. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:11946-11975.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 11946-11975
-
-
MacKerell Jr., A.D.1
Wiorkiewicz-Kuczera, J.2
Karplus, M.3
-
35
-
-
0031577316
-
Theoretical studies of an exceptionally stable RNA tetraloop: Observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics
-
Miller, J. L., and P. A. Kollman. 1997. Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. J. Mol Biol. 270:436-450.
-
(1997)
J. Mol Biol.
, vol.270
, pp. 436-450
-
-
Miller, J.L.1
Kollman, P.A.2
-
37
-
-
0028990057
-
The RNP domain: A sequence-specific RNA-binding domain involved in processing and transport of RNA
-
Nagai, K., C. Oubridge, N. Ito, J. Avis, and P. Evans. 1995. The RNP domain: a sequence-specific RNA-binding domain involved in processing and transport of RNA. Trends Biochem. Sci. 20:235-240.
-
(1995)
Trends Biochem. Sci.
, vol.20
, pp. 235-240
-
-
Nagai, K.1
Oubridge, C.2
Ito, N.3
Avis, J.4
Evans, P.5
-
38
-
-
0025221731
-
Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein a
-
Nagai, K., C. Oubridge, T. H. Jessen, J. Li, and P. R. Evans. 1990. Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature. 348:515-520.
-
(1990)
Nature.
, vol.348
, pp. 515-520
-
-
Nagai, K.1
Oubridge, C.2
Jessen, T.H.3
Li, J.4
Evans, P.R.5
-
39
-
-
33847495971
-
GRASP: Graphical Representation and Analysis of Surface Properties
-
Nicholls, A. 1992. GRASP: Graphical Representation and Analysis of Surface Properties. Columbia University, New York.
-
(1992)
Columbia University, New York.
-
-
Nicholls, A.1
-
41
-
-
0028004607
-
Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin
-
Oubridge, C., N. Ito, P. R. Evans, C.-H. Teo, and K. Nagai. 1994. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 372: 432-438.
-
(1994)
Nature.
, vol.372
, pp. 432-438
-
-
Oubridge, C.1
Ito, N.2
Evans, P.R.3
Teo, C.-H.4
Nagai, K.5
-
42
-
-
0030916603
-
Recent solution structures of RNA and its complexes with drugs, peptides and proteins
-
Ramos, A., C. C. Gubser, and G. Varani. 1997. Recent solution structures of RNA and its complexes with drugs, peptides and proteins. Curr. Opin. Struct. Biol. 7:317-323.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 317-323
-
-
Ramos, A.1
Gubser, C.C.2
Varani, G.3
-
43
-
-
0033057703
-
Molecular dynamics studies of U1A-RNA complexes
-
Reyes, C. M., and P. A. Kollman. 1999. Molecular dynamics studies of U1A-RNA complexes. RNA. 5:235-244.
-
(1999)
RNA.
, vol.5
, pp. 235-244
-
-
Reyes, C.M.1
Kollman, P.A.2
-
44
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., G. Ciccotti, 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: 327-341.
-
(1977)
J. Comp. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
45
-
-
0031047683
-
The role of water in protein-DNA interactions
-
Schwabe, J. W. R. 1997. The role of water in protein-DNA interactions. Curr. Opin. Struct. Biol. 7:126-134.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 126-134
-
-
Schwabe, J.W.R.1
-
46
-
-
0023478466
-
CDNA cloning of the human U1 snRNA-associated a protein: Extensive homology between U1 and U2 snRNP-specific proteins
-
Sillekens, P. T. G., W. J. Habets, R. P. Beijer, and W. J. van Venrooij. 1987. CDNA cloning of the human U1 snRNA-associated A protein: extensive homology between U1 and U2 snRNP-specific proteins. EMBO J. 6:3841-3848.
-
(1987)
EMBO J.
, vol.6
, pp. 3841-3848
-
-
Sillekens, P.T.G.1
Habets, W.J.2
Beijer, R.P.3
Van Venrooij, W.J.4
-
47
-
-
84986534166
-
New spherical-cutoff methods for long-range forces in macromolecular simulation
-
Steinbach, P. J., and B. R. Brooks. 1994. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem. 15:667-683.
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 667-683
-
-
Steinbach, P.J.1
Brooks, B.R.2
-
48
-
-
0032101261
-
Interaction of human SRY protein with DNA: A molecular dynamics study
-
Tang, Y., and L. Nilsson. 1998. Interaction of human SRY protein with DNA: a molecular dynamics study. Proteins. 31:417-433.
-
(1998)
Proteins.
, vol.31
, pp. 417-433
-
-
Tang, Y.1
Nilsson, L.2
-
49
-
-
0031217555
-
Molecular dynamics simulations
-
Tidor, B. 1997. Molecular dynamics simulations. Curr. Biol. 7:R525-R527.
-
(1997)
Curr. Biol.
, vol.7
-
-
Tidor, B.1
-
51
-
-
0000810926
-
RNA-protein intermolecular recognition
-
Varani, G. 1997. RNA-protein intermolecular recognition. Ace. Chem. Res. 30:189-195.
-
(1997)
Ace. Chem. Res.
, vol.30
, pp. 189-195
-
-
Varani, G.1
-
52
-
-
0031860374
-
RNA recognition by RNP proteins during RNA processing
-
Varani, G., and K. Nagai. 1998. RNA recognition by RNP proteins during RNA processing. Anna. Rev. Biophys. Biomol. Struct. 27:407-445.
-
(1998)
Anna. Rev. Biophys. Biomol. Struct.
, vol.27
, pp. 407-445
-
-
Varani, G.1
Nagai, K.2
-
54
-
-
0030916948
-
Protein-facilitated RNA folding
-
Weeks, K. M. 1997. Protein-facilitated RNA folding. Curr. Opin. Struct. Biol. 7:336-342.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 336-342
-
-
Weeks, K.M.1
|