-
2
-
-
73349118813
-
2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions
-
2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions. RNA 15: 2129-2146.
-
(2009)
RNA
, vol.15
, pp. 2129-2146
-
-
Bagby, S.C.1
Bergman, N.H.2
Shechner, D.M.3
Yen, C.4
Bartel, D.P.5
-
3
-
-
0027488624
-
Isolation of new ribozymes from a large pool of random sequences
-
Bartel DP, Szostak JW. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261: 1411-1418.
-
(1993)
Science
, vol.261
, pp. 1411-1418
-
-
Bartel, D.P.1
Szostak, J.W.2
-
4
-
-
23744470902
-
Single-molecule RNA folding
-
Bokinsky G, Zhuang X. 2005. Single-molecule RNA folding. Acc Chem Res 38: 566-573.
-
(2005)
Acc Chem Res
, vol.38
, pp. 566-573
-
-
Bokinsky, G.1
Zhuang, X.2
-
6
-
-
58049201323
-
-
University of California at San Francisco, San Francisco
-
Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Crowley M, Walker RC, Zhang W, et al. 2002. AMBER 10. University of California at San Francisco, San Francisco.
-
(2002)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
-
7
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case DA, Cheatham TE III, Darden TA, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling CL, Wang B, Woods RJ. 2005. The Amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.
-
(2005)
J Comput Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.A.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.L.8
Wang, B.9
Woods, R.J.10
-
8
-
-
34249672905
-
Ribozyme catalysis of metabolism in the RNA world
-
Chen X, Li N, Ellington AD. 2007. Ribozyme catalysis of metabolism in the RNA world. Chem Biodivers 4: 633-655.
-
(2007)
Chem Biodivers
, vol.4
, pp. 633-655
-
-
Chen, X.1
Li, N.2
Ellington, A.D.3
-
9
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117: 5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Ferguson, D.M.5
Spellmeyer, D.C.6
Fox, T.7
Caldwell, J.W.8
Kollman, P.A.9
-
10
-
-
57549094825
-
RNA conformational dynamics
-
(ed. D Stoll et al.), pp Elsevier, Oxford, UK.
-
Crothers D. 2001. RNA conformational dynamics. In RNA (ed. D Stoll et al.), pp 61-71. Elsevier, Oxford, UK.
-
(2001)
RNA
, pp. 61-71
-
-
Crothers, D.1
-
11
-
-
0032545158
-
Stepping through an RNA structure: A novel approach to conformational analysis
-
Duarte CM, Pyle AM. 1998. Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol 284: 1465-1478.
-
(1998)
J Mol Biol
, vol.284
, pp. 1465-1478
-
-
Duarte, C.M.1
Pyle, A.M.2
-
12
-
-
0029147392
-
Structurally complex and highly active RNA ligases derived from random RNA sequences
-
Ekland EH, Szostak JW, Bartel DP. 1995. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269: 364-369.
-
(1995)
Science
, vol.269
, pp. 364-369
-
-
Ekland, E.H.1
Szostak, J.W.2
Bartel, D.P.3
-
13
-
-
0025074907
-
In vitro selection of RNA molecules that bind specific ligands
-
Ellington AD, Szostak JW. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
-
(1990)
Nature
, vol.346
, pp. 818-822
-
-
Ellington, A.D.1
Szostak, J.W.2
-
14
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Hsing L, Pedersen LG. 1995. A smooth particle mesh Ewald method. J Chem Phys 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
Hsing, L.5
Pedersen, L.G.6
-
15
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin piston method
-
Feller S, Zhang Y, Pastor R, Brooks B. 1995. Constant pressure molecular dynamics simulation: The Langevin piston method. J Chem Phys 103: 4613-4621.
-
(1995)
J Chem Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.1
Zhang, Y.2
Pastor, R.3
Brooks, B.4
-
18
-
-
0033592981
-
A complex ligase ribozyme evolved in vitro from a group I ribozyme domain
-
Jaeger L, Wright MC, Joyce GF. 1999. A complex ligase ribozyme evolved in vitro from a group I ribozyme domain. Proc Natl Acad Sci 96: 14712-14717.
-
(1999)
Proc Natl Acad Sci
, vol.96
, pp. 14712-14717
-
-
Jaeger, L.1
Wright, M.C.2
Joyce, G.F.3
-
19
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 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
-
20
-
-
33947377391
-
A glimpse of biology's first enzyme
-
Joyce GF. 2007. A glimpse of biology's first enzyme. Science 315: 1507-1508.
-
(2007)
Science
, vol.315
, pp. 1507-1508
-
-
Joyce, G.F.1
-
21
-
-
0033524391
-
Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution
-
Landweber LF, Pokrovskaya ID. 1999. Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution. Proc Natl Acad Sci 96: 173-178.
-
(1999)
Proc Natl Acad Sci
, vol.96
, pp. 173-178
-
-
Landweber, L.F.1
Pokrovskaya, I.D.2
-
22
-
-
0037102491
-
The non-Watson-Crick base pairs and their associated isostericity matrices
-
Leontis NB, Stombaugh J, Westhof E. 2002. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30: 3497-3531.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3497-3531
-
-
Leontis, N.B.1
Stombaugh, J.2
Westhof, E.3
-
23
-
-
29844453234
-
Topology of three-way junctions in folded RNAs
-
Lescoute A, Westhof E. 2006. Topology of three-way junctions in folded RNAs. RNA 12: 83-93.
-
(2006)
RNA
, vol.12
, pp. 83-93
-
-
Lescoute, A.1
Westhof, E.2
-
24
-
-
0035838382
-
Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture
-
Leulliot N, Varani G. 2001. Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture. Biochemistry 40: 7947-7956.
-
(2001)
Biochemistry
, vol.40
, pp. 7947-7956
-
-
Leulliot, N.1
Varani, G.2
-
26
-
-
36449003554
-
Constant pressure molecular dynamics algorithms
-
Martyna GJ, Tobias DJ, Klein ML. 1994. Constant pressure molecular dynamics algorithms. J Chem Phys 101: 4177-4189.
-
(1994)
J Chem Phys
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
27
-
-
0037256766
-
In search of an RNA replicase ribozyme
-
McGinness KE, Joyce GF. 2003. In search of an RNA replicase ribozyme. Chem Biol 10: 5-14.
-
(2003)
Chem Biol
, vol.10
, pp. 5-14
-
-
McGinness, K.E.1
Joyce, G.F.2
-
29
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structure and energetic properties of molecules
-
Pearlman DA, Case DA, Caldwell JW, Ross WR, Cheatham TE III, DeBolt S, Ferguson D, Seibel G, Kollman P. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structure and energetic properties of molecules. Comput Phys Commun 91: 1-41.
-
(1995)
Comput Phys Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.R.4
Cheatham III, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
30
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kaleé L, Schulten K. 2005. Scalable molecular dynamics with NAMD. J Comput Chem 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
Kaleé, L.9
Schulten, K.10
-
32
-
-
40449091092
-
RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
-
Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, et al. 2008. RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA 14: 465-481.
-
(2008)
RNA
, vol.14
, pp. 465-481
-
-
Richardson, J.S.1
Schneider, B.2
Murray, L.W.3
Kapral, G.J.4
Immormino, R.M.5
Headd, J.J.6
Richardson, D.C.7
Ham, D.8
Hershkovits, E.9
Williams, L.D.10
-
33
-
-
0032955410
-
In vitro selection of an allosteric ribozyme that transduces analytes to amplicons
-
Robertson MP, Ellington AD. 1999. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol 17: 62-66.
-
(1999)
Nat Biotechnol
, vol.17
, pp. 62-66
-
-
Robertson, M.P.1
Ellington, A.D.2
-
34
-
-
0034655587
-
Design and optimization of effector-activated ribozyme ligases
-
Robertson MP, Ellington AD. 2000. Design and optimization of effector-activated ribozyme ligases. Nucleic Acids Res 28: 1751-1759.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 1751-1759
-
-
Robertson, M.P.1
Ellington, A.D.2
-
35
-
-
0034936573
-
In vitro selection of nucleoprotein enzymes
-
Robertson MP, Ellington AD. 2001. In vitro selection of nucleoprotein enzymes. Nat Biotechnol 19: 650-655.
-
(2001)
Nat Biotechnol
, vol.19
, pp. 650-655
-
-
Robertson, M.P.1
Ellington, A.D.2
-
36
-
-
33947389130
-
The structural basis of ribozyme-catalyzed RNA assembly
-
Robertson MP, Scott WG. 2007. The structural basis of ribozyme-catalyzed RNA assembly. Science 315: 1549-1550.
-
(2007)
Science
, vol.315
, pp. 1549-1550
-
-
Robertson, M.P.1
Scott, W.G.2
-
37
-
-
0035000517
-
Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings
-
Robertson MP, Hesselberth JR, Ellington AD. 2001. Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings. RNA 7: 513-523.
-
(2001)
RNA
, vol.7
, pp. 513-523
-
-
Robertson, M.P.1
Hesselberth, J.R.2
Ellington, A.D.3
-
38
-
-
0346992203
-
In vitro selection of ribozymes dependent on peptides for activity
-
Robertson MP, Knudsen SM, Ellington AD. 2004. In vitro selection of ribozymes dependent on peptides for activity. RNA 10: 114-127.
-
(2004)
RNA
, vol.10
, pp. 114-127
-
-
Robertson, M.P.1
Knudsen, S.M.2
Ellington, A.D.3
-
39
-
-
0033581938
-
A ribozyme that lacks cytidine
-
Rogers J, Joyce GF. 1999. A ribozyme that lacks cytidine. Nature 402: 323-325.
-
(1999)
Nature
, vol.402
, pp. 323-325
-
-
Rogers, J.1
Joyce, G.F.2
-
40
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys 23: 327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
41
-
-
0033024177
-
Molecular dynamics simulations of biomolecules: Long-range electrostatic effects
-
Sagui C, Darden TA. 1999. Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Annu Rev Biophys Biomol Struct 28: 155-179.
-
(1999)
Annu Rev Biophys Biomol Struct
, vol.28
, pp. 155-179
-
-
Sagui, C.1
Darden, T.A.2
-
42
-
-
0030930760
-
Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
-
Sawaya MR, Prasad R, Wilson S, Kraut J, Pelletier H. 1997. Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism. Biochemistry 36: 11205-11215.
-
(1997)
Biochemistry
, vol.36
, pp. 11205-11215
-
-
Sawaya, M.R.1
Prasad, R.2
Wilson, S.3
Kraut, J.4
Pelletier, H.5
-
44
-
-
34247242053
-
Structures of RNA switches: Insight into molecular recognition and tertiary structure
-
Schwalbe H, Buck J. Fürtig B, Noeske J, Wöhnert J. 2007. Structures of RNA switches: Insight into molecular recognition and tertiary structure. Angew Chem Int Ed 46: 1212-1219.
-
(2007)
Angew Chem Int Ed
, vol.46
, pp. 1212-1219
-
-
Schwalbe, H.1
Buck, J.2
Fürtig, B.3
Noeske, J.4
Wöhnert, J.5
-
45
-
-
70849121359
-
Crystal structure of the catalytic core of an RNA-polymerase ribozyme
-
Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP. 2009. Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science 326: 1271-1275.
-
(2009)
Science
, vol.326
, pp. 1271-1275
-
-
Shechner, D.M.1
Grant, R.A.2
Bagby, S.C.3
Koldobskaya, Y.4
Piccirilli, J.A.5
Bartel, D.P.6
-
46
-
-
0141974927
-
Global mapping of nucleic acid conformational space: Dinucleoside monophosphate conformations and transition pathways among conformational classes
-
Sims GE, Kim SH. 2003. Global mapping of nucleic acid conformational space: Dinucleoside monophosphate conformations and transition pathways among conformational classes. Nucleic Acids Res 31: 5607-5616.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5607-5616
-
-
Sims, G.E.1
Kim, S.H.2
-
47
-
-
0027411261
-
DNA- And RNA-dependent DNA polymerases
-
Steitz TA. 1993. DNA- and RNA-dependent DNA polymerases. Curr Opin Struct Biol 3: 31-38.
-
(1993)
Curr Opin Struct Biol
, vol.3
, pp. 31-38
-
-
Steitz, T.A.1
-
48
-
-
0027184481
-
A general two-metal-ion mechanism for catalytic RNA
-
Steitz TA, Steitz JA. 1993. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci 90: 6498-6502.
-
(1993)
Proc Natl Acad Sci
, vol.90
, pp. 6498-6502
-
-
Steitz, T.A.1
Steitz, J.A.2
-
50
-
-
34548401692
-
Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure
-
Wadley LM, Keating KS, Duarte CM, Pyle AM. 2007. Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure. J Mol Biol 372: 942-957.
-
(2007)
J Mol Biol
, vol.372
, pp. 942-957
-
-
Wadley, L.M.1
Keating, K.S.2
Duarte, C.M.3
Pyle, A.M.4
-
51
-
-
0033784534
-
Induced fit in RNA-protein recognition
-
Williamson JR. 2000. Induced fit in RNA-protein recognition. Nat Struct Biol 7: 834-837.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 834-837
-
-
Williamson, J.R.1
-
52
-
-
77950238461
-
Taking femtosecond snapshots of RNA conformational dynamics and complexity
-
Xia T. 2008. Taking femtosecond snapshots of RNA conformational dynamics and complexity. Curr Opin Chem Biol 2: 1-8.
-
(2008)
Curr Opin Chem Biol
, vol.2
, pp. 1-8
-
-
Xia, T.1
|