Published in Science on March 29, 2001
RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
Natively unfolded proteins: a point where biology waits for physics. Protein Sci (2002) 6.91
Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA. Nature (2008) 6.25
5S Ribosomal RNA Database. Nucleic Acids Res (2002) 5.95
tRNA dynamics on the ribosome during translation. Proc Natl Acad Sci U S A (2004) 5.38
Understanding protein non-folding. Biochim Biophys Acta (2010) 4.33
Following translation by single ribosomes one codon at a time. Nature (2008) 4.14
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. J Math Biol (2007) 4.12
What recent ribosome structures have revealed about the mechanism of translation. Nature (2009) 4.01
Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev (2005) 3.78
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J (2004) 3.69
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci U S A (2003) 3.64
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol Cell (2008) 3.58
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics (2008) 3.55
An active role for tRNA in decoding beyond codon:anticodon pairing. Science (2005) 3.49
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Nature (2010) 3.48
Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev (2011) 2.97
Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A (2005) 2.91
Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes Dev (2003) 2.89
Kinetically competent intermediates in the translocation step of protein synthesis. Mol Cell (2007) 2.89
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature (2010) 2.85
Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes Dev (2003) 2.77
GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J (2009) 2.71
Fidelity at the molecular level: lessons from protein synthesis. Cell (2009) 2.65
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
Ribosome biogenesis and the translation process in Escherichia coli. Microbiol Mol Biol Rev (2007) 2.59
Structural basis for mRNA and tRNA positioning on the ribosome. Proc Natl Acad Sci U S A (2006) 2.55
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. EMBO J (2007) 2.48
The process of mRNA-tRNA translocation. Proc Natl Acad Sci U S A (2007) 2.45
Structural insights into peptide bond formation. Proc Natl Acad Sci U S A (2002) 2.40
Following movement of the L1 stalk between three functional states in single ribosomes. Proc Natl Acad Sci U S A (2009) 2.40
Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science (2009) 2.33
The hybrid state of tRNA binding is an authentic translation elongation intermediate. Nat Struct Mol Biol (2006) 2.32
Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat Struct Mol Biol (2010) 2.30
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. Insect Mol Biol (2006) 2.30
Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res (2002) 2.24
A new system for naming ribosomal proteins. Curr Opin Struct Biol (2014) 2.18
The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. RNA (2003) 2.14
Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure (2008) 2.11
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci U S A (2009) 2.04
The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. Genome Res (2002) 2.03
RNA SHAPE analysis in living cells. Nat Chem Biol (2012) 2.02
Frameshifting RNA pseudoknots: structure and mechanism. Virus Res (2008) 2.02
Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A (2005) 2.01
The tmRDB and SRPDB resources. Nucleic Acids Res (2006) 2.01
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proc Natl Acad Sci U S A (2010) 1.99
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA (2007) 1.98
Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res (2005) 1.97
Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol (2001) 1.94
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA (2010) 1.91
Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA. Proc Natl Acad Sci U S A (2001) 1.91
Irreversible chemical steps control intersubunit dynamics during translation. Proc Natl Acad Sci U S A (2008) 1.88
A hierarchical model for evolution of 23S ribosomal RNA. Nature (2009) 1.87
RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes Dev (2009) 1.87
Structure and dynamics of a processive Brownian motor: the translating ribosome. Annu Rev Biochem (2010) 1.84
Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science (2006) 1.83
Intersubunit movement is required for ribosomal translocation. Proc Natl Acad Sci U S A (2007) 1.83
Fluctuations of transfer RNAs between classical and hybrid states. Biophys J (2007) 1.82
Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications. Proc Natl Acad Sci U S A (2004) 1.81
Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res (2001) 1.80
A synonymous polymorphism in a common MDR1 (ABCB1) haplotype shapes protein function. Biochim Biophys Acta (2009) 1.79
Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs. Nucleic Acids Res (2004) 1.79
Structural dynamics of the ribosome. Curr Opin Chem Biol (2008) 1.79
Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease. EMBO J (2001) 1.77
One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol (2012) 1.77
Navigating the ribosome's metastable energy landscape. Trends Biochem Sci (2009) 1.74
Protein synthesis by single ribosomes. RNA (2003) 1.74
Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications. ACS Chem Biol (2007) 1.73
Mutations in the 16S rRNA genes of Helicobacter pylori mediate resistance to tetracycline. J Bacteriol (2002) 1.70
POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res (2003) 1.69
The role of fluctuations in tRNA selection by the ribosome. Proc Natl Acad Sci U S A (2007) 1.69
Architecture of the large subunit of the mammalian mitochondrial ribosome. Nature (2013) 1.69
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. Proc Natl Acad Sci U S A (2010) 1.68
The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Nucleic Acids Res (2007) 1.65
A steric block in translation caused by the antibiotic spectinomycin. ACS Chem Biol (2007) 1.64
Protein synthesis by ribosomes with tethered subunits. Nature (2015) 1.63
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res (2003) 1.63
tRNA properties help shape codon pair preferences in open reading frames. Nucleic Acids Res (2006) 1.63
Exploring global motions and correlations in the ribosome. Biophys J (2005) 1.62
Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing. Nucleic Acids Res (2009) 1.61
Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy. Structure (2015) 1.61
GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Mol Cell (2009) 1.59
Structural rearrangements of the ribosome at the tRNA proofreading step. Nat Struct Mol Biol (2010) 1.59
RNA misfolding and the action of chaperones. Front Biosci (2008) 1.59
Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. RNA (2003) 1.58
X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Proc Natl Acad Sci U S A (2003) 1.58
Optimization of ribosome structure and function by rRNA base modification. PLoS One (2007) 1.57
A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. Proc Natl Acad Sci U S A (2001) 1.57
Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1. RNA (2002) 1.56
The origins of the RNA world. Cold Spring Harb Perspect Biol (2012) 1.55
Long-distance RNA-RNA interactions in plant virus gene expression and replication. Annu Rev Phytopathol (2006) 1.53
The domains of a cholesterol-dependent cytolysin undergo a major FRET-detected rearrangement during pore formation. Proc Natl Acad Sci U S A (2005) 1.52
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res (2009) 1.52
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc Natl Acad Sci U S A (2007) 1.52
Structural analysis of kasugamycin inhibition of translation. Nat Struct Mol Biol (2006) 1.51
A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol Mol Biol Rev (2009) 1.50
Internal strain regulates the nucleotide binding site of the kinesin leading head. Proc Natl Acad Sci U S A (2007) 1.50
Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A (1978) 32.65
Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol (1981) 29.04
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev (1983) 23.08
Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol (1985) 16.21
X-ray crystal structures of 70S ribosome functional complexes. Science (1999) 10.51
Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res (1980) 9.50
Structure of ribosomal RNA. Annu Rev Biochem (1984) 9.44
Construction and fine mapping of recombinant plasmids containing the rrnB ribosomal RNA operon of E. coli. Plasmid (1981) 9.00
Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature (1987) 8.96
Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. J Mol Biol (1986) 7.87
Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A (1980) 7.80
Intermediate states in the movement of transfer RNA in the ribosome. Nature (1989) 7.30
Secondary structure model for 23S ribosomal RNA. Nucleic Acids Res (1981) 7.12
Secondary structure of 16S ribosomal RNA. Science (1981) 6.52
Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol (1988) 6.38
Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell (1989) 5.79
Protection of specific sites in 16 S RNA from chemical modification by association of 30 S and 50 S ribosomes. J Mol Biol (1977) 5.66
The path of messenger RNA through the ribosome. Cell (2001) 5.65
Mechanism of ribosomal subunit association: discrimination of specific sites in 16 S RNA essential for association activity. J Mol Biol (1979) 4.88
rII cistrons of bacteriophage T4. DNA sequence around the intercistronic divide and positions of genetic landmarks. J Mol Biol (1981) 4.76
Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell (1986) 4.65
A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature (1995) 4.59
Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA. Nature (1988) 4.53
Chloramphenicol, erythromycin, carbomycin and vernamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA. Biochimie (1987) 4.47
The nucleotide sequence of a rat 18 S ribosomal ribonucleic acid gene and a proposal for the secondary structure of 18 S ribosomal ribonucleic acid. J Biol Chem (1984) 4.00
Ribosomes and translation. Annu Rev Biochem (1997) 3.87
A functional pseudoknot in 16S ribosomal RNA. EMBO J (1991) 3.59
Identification of an RNA-protein bridge spanning the ribosomal subunit interface. Science (1999) 3.31
Model for the three-dimensional folding of 16 S ribosomal RNA. J Mol Biol (1988) 3.24
A "bulged" double helix in a RNA-protein contact site. Proc Natl Acad Sci U S A (1981) 3.16
RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA. Science (1989) 2.97
Higher order structure in ribosomal RNA. EMBO J (1986) 2.97
Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. J Mol Biol (1990) 2.90
Functional modification of 16S ribosomal RNA by kethoxal. Proc Natl Acad Sci U S A (1972) 2.74
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat Struct Biol (1998) 2.71
Topography of 16S RNA in 30S ribosomal subunits. Nucleotide sequences and location of sites of reaction with kethoxal. Biochemistry (1974) 2.67
Mutations in 16S ribosomal RNA disrupt antibiotic--RNA interactions. EMBO J (1989) 2.54
Altered topography of 16S RNA in the inactive form of Escherichia coli 30S ribosomal subunits. Biochemistry (1978) 2.44
Amino-acid sequence of glyceraldehyde 3-phosphate dehydrogenase from lobster muscle. Nature (1967) 2.40
Interaction of translation initiation factor 3 with the 30S ribosomal subunit. Mol Cell (2001) 2.34
Sites of interaction of the CCA end of peptidyl-tRNA with 23S rRNA. Proc Natl Acad Sci U S A (1991) 2.34
The structure of the RNA binding site of ribosomal proteins S8 and S15. J Biol Chem (1979) 2.24
Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center. Proc Natl Acad Sci U S A (1984) 2.22
Nucleotide sequence of the 3' terminus of E. coli 16S ribosomal RNA. Mol Biol Rep (1974) 2.13
A fragment of 23S RNA containing a nucleotide sequence complementary to a region of 5S RNA. FEBS Lett (1975) 2.07
Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit. Proc Natl Acad Sci U S A (2001) 2.06
Aminoacyl esterase activity of the Tetrahymena ribozyme. Science (1992) 2.06
Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing. Cell (1998) 2.06
Dynamics of in vitro assembly of 16 S rRNA into 30 S ribosomal subunits. J Mol Biol (1993) 2.02
A cold-sensitive mutation in 16S rRNA provides evidence for helical switching in ribosome assembly. Genes Dev (1993) 2.00
Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA (1995) 1.98
Interconversion of active and inactive 30 S ribosomal subunits is accompanied by a conformational change in the decoding region of 16 S rRNA. J Mol Biol (1986) 1.97
Interaction of antibiotics with A- and P-site-specific bases in 16S ribosomal RNA. EMBO J (1991) 1.96
Mutations in ribosomal proteins S4 and S12 influence the higher order structure of 16 S ribosomal RNA. J Mol Biol (1989) 1.94
Dominant lethal mutations in a conserved loop in 16S rRNA. Proc Natl Acad Sci U S A (1990) 1.91
Footprinting the sites of interaction of antibiotics with catalytic group I intron RNA. Science (1993) 1.90
Footprinting mRNA-ribosome complexes with chemical probes. EMBO J (1994) 1.84
Clathrin self-assembly is mediated by a tandemly repeated superhelix. Nature (1999) 1.84
Localization of the binding site for protein S4 on 16 S ribosomal RNA by chemical and enzymatic probing and primer extension. J Mol Biol (1986) 1.83
Isolation of temperature-sensitive mutants of 16 S rRNA in Escherichia coli. J Mol Biol (1989) 1.82
Protection of specific sites in 23 S and 5 S RNA from chemical modification by association of 30 S and 50 S ribosomes. J Mol Biol (1979) 1.82
Orientation of the bacteriorhodopsin chromophore probed by polarized Fourier transform infrared difference spectroscopy. Biochemistry (1986) 1.76
Specific protection of 16 S rRNA by translational initiation factors. J Mol Biol (1995) 1.76
Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA. EMBO J (1994) 1.76
Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP. Science (2000) 1.70
Molecular basis of tetracycline action: identification of analogs whose primary target is not the bacterial ribosome. Antimicrob Agents Chemother (1991) 1.69
EF-G-catalyzed translocation of anticodon stem-loop analogs of transfer RNA in the ribosome. EMBO J (1998) 1.68
Structure of 5 S ribosomal RNA from Escherichia coli: identification of kethoxal-reactive sites in the A and B conformations. J Mol Biol (1979) 1.66
Suppression of a cold-sensitive mutation in 16S rRNA by overexpression of a novel ribosome-binding factor, RbfA. Genes Dev (1995) 1.66
Interaction of ribosomal proteins S5, S6, S11, S12, S18 and S21 with 16 S rRNA. J Mol Biol (1988) 1.63
Defining the structural requirements for a helix in 23 S ribosomal RNA that confers erythromycin resistance. J Mol Biol (1989) 1.57
Single-wavelength anomalous diffraction phasing revisited. Acta Crystallogr D Biol Crystallogr (2000) 1.54
Molecular movement inside the translational engine. Cell (1998) 1.53
Alteration of polynucleotide secondary structure by ribosomal protein S1. Proc Natl Acad Sci U S A (1976) 1.49
Reconstitution of functional 50S ribosomes from in vitro transcripts of Bacillus stearothermophilus 23S rRNA. Biochemistry (1999) 1.47
Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site. Science (1995) 1.46
Structures of complexes of 5S RNA with ribosomal proteins L5, L18 and L25 from Escherichia coli: identification of kethoxal-reactive sites on the 5S RNA. J Mol Biol (1979) 1.45
Independent in vitro assembly of a ribonucleoprotein particle containing the 3' domain of 16S rRNA. Proc Natl Acad Sci U S A (1994) 1.43
Evidence for a tyrosine protonation change during the primary phototransition of bacteriorhodopsin at low temperature. Proc Natl Acad Sci U S A (1986) 1.39
A biophysical study of integral membrane protein folding. Biochemistry (1997) 1.35
Mutations at nucleotides G2251 and U2585 of 23 S rRNA perturb the peptidyl transferase center of the ribosome. J Mol Biol (1997) 1.34
Hydroxyl radical cleavage of tRNA in the ribosomal P site. Proc Natl Acad Sci U S A (1992) 1.34
Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nat Struct Biol (1998) 1.33
Protection of ribosomal RNA from kethoxal in polyribosomes. Implication of specific sites in ribosome function. J Mol Biol (1983) 1.33
Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits. J Mol Biol (1999) 1.32
Streptomycin-resistant and streptomycin-dependent mutants of the extreme thermophile Thermus thermophilus. J Mol Biol (2001) 1.32
Mapping the inside of the ribosome with an RNA helical ruler. Science (1997) 1.31
Interaction of proteins S16, S17 and S20 with 16 S ribosomal RNA. J Mol Biol (1988) 1.29
In vitro reconstitution of 30S ribosomal subunits using complete set of recombinant proteins. Methods Enzymol (2000) 1.29
Probing the conformation of 18S rRNA in yeast 40S ribosomal subunits with kethoxal. Biochemistry (1984) 1.28
Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA. Science (1998) 1.27
Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4. Proc Natl Acad Sci U S A (1995) 1.27
Directed hydroxyl radical probing of RNA from iron(II) tethered to proteins in ribonucleoprotein complexes. Methods Enzymol (2000) 1.26