-
1
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein, F., Koetzle, T., Williams, G., Meyer Jr., E., Brice, M., Rodgers, J., Kennard, O., Shimanouchi, T., and Tasumi, M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112: 535-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.1
Koetzle, T.2
Williams, G.3
Meyer Jr., E.4
Brice, M.5
Rodgers, J.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
2
-
-
2942571539
-
The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
Cannone, J., Subramanian, S., Schnare, M., Collett, J., D'Souza, L., Du, Y., Feng, B., Lin, N., Madabusi, L., Muller, K., et al. 2002. The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 2
-
-
Cannone, J.1
Subramanian, S.2
Schnare, M.3
Collett, J.4
D'Souza, L.5
Du, Y.6
Feng, B.7
Lin, N.8
Madabusi, L.9
Muller, K.10
-
3
-
-
0029796982
-
RNA tertiary structure mediation by adenosine platforms
-
Cate, J., Gooding, A., Podell, E., Zhou, K., Golden, B., Szewczak, A., Kundrot, C., Cech, T., and Doudna, J. 1996. RNA tertiary structure mediation by adenosine platforms. Science 273: 1696-1699.
-
(1996)
Science
, vol.273
, pp. 1696-1699
-
-
Cate, J.1
Gooding, A.2
Podell, E.3
Zhou, K.4
Golden, B.5
Szewczak, A.6
Kundrot, C.7
Cech, T.8
Doudna, J.9
-
4
-
-
0035073865
-
A universal mode of helix packing in RNA
-
Doherty, E.A., Batey, R.T., Masquida, B., and Doudna, J.A. 2001. A universal mode of helix packing in RNA. Nat. Struct. Biol. 8: 339-343.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 339-343
-
-
Doherty, E.A.1
Batey, R.T.2
Masquida, B.3
Doudna, J.A.4
-
5
-
-
50449121567
-
Evidence of common regularities in the composition of pentose nucleic acids
-
Elson, D. and Chargaff, E. 1955. Evidence of common regularities in the composition of pentose nucleic acids. Biochim. Biophys. Acta 17: 367-376.
-
(1955)
Biochim. Biophys. Acta
, vol.17
, pp. 367-376
-
-
Elson, D.1
Chargaff, E.2
-
6
-
-
0030900384
-
Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes
-
Galtier, N. and Lobry, J. 1997. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44: 632-636.
-
(1997)
J. Mol. Evol.
, vol.44
, pp. 632-636
-
-
Galtier, N.1
Lobry, J.2
-
7
-
-
0034405491
-
A story: Unpaired adenosine bases in ribosomal RNAs
-
Gutell, R.R., Cannone, J.J., Shang, Z., Du, Y., and Serra, M.J. 2000. A story: Unpaired adenosine bases in ribosomal RNAs. J. Mol. Biol. 304: 335-354.
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 335-354
-
-
Gutell, R.R.1
Cannone, J.J.2
Shang, Z.3
Du, Y.4
Serra, M.J.5
-
8
-
-
0036600570
-
The accuracy of ribosomal RNA comparative structure models
-
Gutell, R., Lee, J., and Cannone, J. 2002. The accuracy of ribosomal RNA comparative structure models. Curr. Opin. Struct. Biol. 12: 301-310.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 301-310
-
-
Gutell, R.1
Lee, J.2
Cannone, J.3
-
9
-
-
5444276316
-
Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication
-
Guy, L. and Roten, C. 2004. Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication. Gene 340: 45-52.
-
(2004)
Gene
, vol.340
, pp. 45-52
-
-
Guy, L.1
Roten, C.2
-
10
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker, I., Fontana, W., Stadler, P., Bonhoeffer, L., Tacker, M., and Schuster, P. 1994. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125: 167-188.
-
(1994)
Monatsh. Chem.
, vol.125
, pp. 167-188
-
-
Hofacker, I.1
Fontana, W.2
Stadler, P.3
Bonhoeffer, L.4
Tacker, M.5
Schuster, P.6
-
11
-
-
0035220937
-
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
-
Knight, R., Freeland, S., and Landweber, L. 2001. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol. 2: http://genomebiology.com.
-
(2001)
Genome Biol.
, vol.2
-
-
Knight, R.1
Freeland, S.2
Landweber, L.3
-
12
-
-
4344641945
-
Bayesfold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences
-
Knight, R., Birmingham, A., and Yarus, M. 2004. Bayesfold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA 10: 1323-1336.
-
(2004)
RNA
, vol.10
, pp. 1323-1336
-
-
Knight, R.1
Birmingham, A.2
Yarus, M.3
-
13
-
-
0034006790
-
Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine
-
Lao, P. and Forsdyke, D. 2000. Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res. 10: 228-236.
-
(2000)
Genome Res.
, vol.10
, pp. 228-236
-
-
Lao, P.1
Forsdyke, D.2
-
14
-
-
17844366343
-
Recurrent structural RNA motifs, isostericity matrices, and sequence alignments
-
Lescoute, A., Leontis, N.B., Massire, C., and Westhof, E. 2005. Recurrent structural RNA motifs, isostericity matrices, and sequence alignments. Nucleic Acids Res. 33: 2395-2409.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2395-2409
-
-
Lescoute, A.1
Leontis, N.B.2
Massire, C.3
Westhof, E.4
-
15
-
-
0031593216
-
Influence of genomic G+C content on average aminoacid composition of proteins from 59 bacterial species
-
Lobry, J. 1997. Influence of genomic G+C content on average aminoacid composition of proteins from 59 bacterial species. Gene 205: 309-316.
-
(1997)
Gene
, vol.205
, pp. 309-316
-
-
Lobry, J.1
-
16
-
-
0037179524
-
Asymmetric directional mutation pressures in bacteria
-
Lobry, J. and Sueoka, N. 2002. Asymmetric directional mutation pressures in bacteria. Genome Biol. 3: http://genomebiology.com.
-
(2002)
Genome Biol.
, vol.3
-
-
Lobry, J.1
Sueoka, N.2
-
17
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews, D.H., Sabina, J., Zuker, M., and Turner, D. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.4
-
18
-
-
0029129682
-
Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: Thermodynamic and spectroscopic applications
-
Molinaro, M. and Tinoco Jr., I. 1995. Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: Thermodynamic and spectroscopic applications. Nucleic Acids Res. 23: 3056-3063.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 3056-3063
-
-
Molinaro, M.1
Tinoco Jr., I.2
-
19
-
-
0013596021
-
The guanine and cytosine content of genomic DNA and bacterial evolution
-
Muto,A. and Osawa, S. 1987.The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. 84: 166-169.
-
(1987)
Proc. Natl. Acad. Sci.
, vol.84
, pp. 166-169
-
-
Muto, A.1
Osawa, S.2
-
20
-
-
0035942248
-
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif
-
Nissen, P., Ippolito, J., Ban, N., Moore, P., and Steitz, T. 2001. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl. Acad. Sci. 98: 4899-4903.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 4899-4903
-
-
Nissen, P.1
Ippolito, J.2
Ban, N.3
Moore, P.4
Steitz, T.5
-
21
-
-
0027049243
-
The kinemage: A tool for scientific communication
-
Richardson, D. and Richardson, J. 1992. The kinemage: A tool for scientific communication. Protein Sci. 1: 3-9.
-
(1992)
Protein Sci.
, vol.1
, pp. 3-9
-
-
Richardson, D.1
Richardson, J.2
-
22
-
-
0030759786
-
Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence
-
Schultes, E., Hraber, P., and LaBean, T. 1997. Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence. RNA 3: 792-806.
-
(1997)
RNA
, vol.3
, pp. 792-806
-
-
Schultes, E.1
Hraber, P.2
LaBean, T.3
-
23
-
-
0033013683
-
Estimating the contributions of selection and selforganization in RNA secondary structure
-
_. 1999. Estimating the contributions of selection and selforganization in RNA secondary structure. J. Mol. Evol. 49: 76-83.
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 76-83
-
-
-
24
-
-
0028196714
-
From sequences to shapes and back: A case study in RNA secondary structures
-
Schuster, P., Fontana, W., Stadler, P., and Hofacker, I. 1994. From sequences to shapes and back: A case study in RNA secondary structures. Proc. R. Soc. Lond. B Biol. Sci. 255: 279-284.
-
(1994)
Proc. R. Soc. Lond. B Biol. Sci.
, vol.255
, pp. 279-284
-
-
Schuster, P.1
Fontana, W.2
Stadler, P.3
Hofacker, I.4
-
25
-
-
0033745103
-
Nucleotide bias causes a genomewide bias in the amino acid composition of proteins
-
Singer, G. and Hickey, D. 2000. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17:1581-1588.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 1581-1588
-
-
Singer, G.1
Hickey, D.2
-
26
-
-
73049156042
-
Compositional correlation between deoxyribonucleic acid and protein
-
Sueoka, N. 1961. Compositional correlation between deoxyribonucleic acid and protein. Cold Spring Harb. Symp. Quant. Biol. 26: 35-43.
-
(1961)
Cold Spring Harb. Symp. Quant. Biol.
, vol.26
, pp. 35-43
-
-
Sueoka, N.1
-
27
-
-
3643052747
-
On the genetic basis of variation and heterogeneity of DNA base composition
-
_. 1962. On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. 48: 582-592.
-
(1962)
Proc. Natl. Acad. Sci.
, vol.48
, pp. 582-592
-
-
-
28
-
-
0023991945
-
Directional mutation pressure and neutral molecular evolution
-
_. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. 85: 2653-2657.
-
(1988)
Proc. Natl. Acad. Sci.
, vol.85
, pp. 2653-2657
-
-
-
29
-
-
0033053160
-
Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of at and GC
-
_. 1999. Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of AT and GC. J. Mol. Evol. 49: 49-62.
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 49-62
-
-
-
30
-
-
0030292964
-
RNA enzymes: Putting together a large ribozyme
-
Tinoco Jr., I. 1996. RNA enzymes: Putting together a large ribozyme. Curr. Biol. 6: 1374-1376.
-
(1996)
Curr. Biol.
, vol.6
, pp. 1374-1376
-
-
Tinoco Jr., I.1
-
31
-
-
0023973247
-
CUUCGG hairpins: Extraordinarily stable RNA secondary structures associated with various biochemical processes
-
Tuerk, C., Gauss, P., Thermes, C., Groebe, D., Gayle, M., Guild, N., Stormo, G., d'Aubenton-Carafa, Y., Uhlenbeck, O., Tinoco Jr., I., et al. 1988. CUUCGG hairpins: Extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. Natl. Acad. Sci. 85: 1364-1368.
-
(1988)
Proc. Natl. Acad. Sci.
, vol.85
, pp. 1364-1368
-
-
Tuerk, C.1
Gauss, P.2
Thermes, C.3
Groebe, D.4
Gayle, M.5
Guild, N.6
Stormo, G.7
D'Aubenton-Carafa, Y.8
Uhlenbeck, O.9
Tinoco Jr., I.10
-
32
-
-
0036606141
-
Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes
-
Wang, H. and Hickey, D. 2002. Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res. 30: 2501-2507.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2501-2507
-
-
Wang, H.1
Hickey, D.2
-
33
-
-
6044241907
-
Evolution of RNA architecture
-
Westhof, E. and Massire, C. 2004. Evolution of RNA architecture. Science 306: 62-63.
-
(2004)
Science
, vol.306
, pp. 62-63
-
-
Westhof, E.1
Massire, C.2
-
34
-
-
0034699518
-
Structure of the 30S ribosomal subunit
-
Wimberly, B., Brodersen, D., Clemons Jr., W., Morgan-Warren, R., Carter, A., Vonrhein, C., Hartsch, R., and Ramakrishnan, V. 2000. Structure of the 30S ribosomal subunit. Nature 407: 327-339.
-
(2000)
Nature
, vol.407
, pp. 327-339
-
-
Wimberly, B.1
Brodersen, D.2
Clemons Jr., W.3
Morgan-Warren, R.4
Carter, A.5
Vonrhein, C.6
Hartsch, R.7
Ramakrishnan, V.8
-
35
-
-
0025047647
-
Architecture of ribosomal RNA: Constraints on the sequence of "tetra-loops"
-
Woese, C.R., Winker, S., and Gutell, R.R. 1990. Architecture of ribosomal RNA: Constraints on the sequence of "tetra-loops." Proc. Natl. Acad. Sci. 87: 8467-8471.
-
(1990)
Proc. Natl. Acad. Sci.
, vol.87
, pp. 8467-8471
-
-
Woese, C.R.1
Winker, S.2
Gutell, R.R.3
-
36
-
-
0035162598
-
The European large subunit ribosomal RNA database
-
Wuyts, J., De Rijk, P., Van de Peer, Y., Winkelmans, T., and De Wachter, R. 2001. The European large subunit ribosomal RNA database. Nucleic Acids Res. 29: 175-177.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 175-177
-
-
Wuyts, J.1
De Rijk, P.2
Van De Peer, Y.3
Winkelmans, T.4
De Wachter, R.5
-
37
-
-
0036081020
-
The European database on small subunit ribosomal RNA
-
Wuyts, J., Van de Peer, Y., Winkelmans, T., and De Wachter, R. 2002. The European database on small subunit ribosomal RNA. Nucleic Acids Res. 30: 183-185.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 183-185
-
-
Wuyts, J.1
Van De Peer, Y.2
Winkelmans, T.3
De Wachter, R.4
-
38
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker, M. and Stiegler, P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9: 133-148.
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
|