Published in J Mol Biol on August 09, 2002
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A (2005) 2.91
Powering through ribosome assembly. RNA (2009) 2.19
The ribosome challenge to the RNA world. J Mol Evol (2015) 2.10
An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis? Mol Cell (2009) 2.03
Mitochondrial translation and beyond: processes implicated in combined oxidative phosphorylation deficiencies. J Biomed Biotechnol (2010) 2.01
Unifying measures of gene function and evolution. Proc Biol Sci (2006) 1.55
Evolution of the ribosome at atomic resolution. Proc Natl Acad Sci U S A (2014) 1.54
Origin and evolution of the ribosome. Cold Spring Harb Perspect Biol (2010) 1.47
A structural model for the large subunit of the mammalian mitochondrial ribosome. J Mol Biol (2006) 1.46
Oxazolidinones inhibit cellular proliferation via inhibition of mitochondrial protein synthesis. Antimicrob Agents Chemother (2005) 1.44
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Nat Struct Mol Biol (2010) 1.42
Structure of a mitochondrial ribosome with minimal RNA. Proc Natl Acad Sci U S A (2009) 1.38
Bocavirus episome in infected human tissue contains non-identical termini. PLoS One (2011) 1.29
Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution. RNA (2006) 1.24
Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA (2008) 1.21
Structural specificity conferred by a group I RNA peripheral element. Proc Natl Acad Sci U S A (2005) 1.19
The origin and evolution of the ribosome. Biol Direct (2008) 1.10
The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. PLoS One (2012) 1.04
Structural relationships among the ribosomal stalk proteins from the three domains of life. J Mol Evol (2008) 1.04
Structural aspects of mitochondrial translational apparatus. Curr Opin Struct Biol (2012) 1.00
Improved tRNA prediction in the American house dust mite reveals widespread occurrence of extremely short minimal tRNAs in acariform mites. BMC Genomics (2009) 0.95
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center. Nucleic Acids Res (2009) 0.93
VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinformatics (2010) 0.92
Protein content of minimal and ancestral ribosome. RNA (2005) 0.91
Comparative analysis of dinoflagellate chloroplast genomes reveals rRNA and tRNA genes. BMC Genomics (2006) 0.90
Initial bridges between two ribosomal subunits are formed within 9.4 milliseconds, as studied by time-resolved cryo-EM. Proc Natl Acad Sci U S A (2014) 0.89
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. BMC Bioinformatics (2010) 0.89
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation. J R Soc Interface (2009) 0.88
Mitochondrial protein synthesis: figuring the fundamentals, complexities and complications, of mammalian mitochondrial translation. FEBS Lett (2014) 0.87
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Res (2007) 0.87
Sequence and structural evolution of the KsgA/Dim1 methyltransferase family. BMC Res Notes (2008) 0.86
Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes. Genome Biol Evol (2015) 0.86
Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors. Front Genet (2014) 0.85
Toward ribosomal RNA catalytic activity in the absence of protein. J Mol Evol (2007) 0.84
Molecular paleontology: a biochemical model of the ancestral ribosome. Nucleic Acids Res (2013) 0.84
Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations. Nucleic Acids Res (2013) 0.84
Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J (2015) 0.82
Trans-splicing and RNA editing of LSU rRNA in Diplonema mitochondria. Nucleic Acids Res (2013) 0.82
The ancient heart of the ribosomal large subunit: a response to Caetano-Anolles. J Mol Evol (2015) 0.81
Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics. RNA (2015) 0.81
Evolutionary relationships among Chlamydophila abortus variant strains inferred by rRNA secondary structure-based phylogeny. PLoS One (2011) 0.79
The Proto-Ribosome: an ancient nano-machine for peptide bond formation. Isr J Chem (2010) 0.79
Assembly constraints drive co-evolution among ribosomal constituents. Nucleic Acids Res (2015) 0.78
Systems biology perspectives on minimal and simpler cells. Microbiol Mol Biol Rev (2014) 0.78
The RICE MINUTE-LIKE1 (RML1) gene, encoding a ribosomal large subunit protein L3B, regulates leaf morphology and plant architecture in rice. J Exp Bot (2016) 0.76
The 55S mammalian mitochondrial ribosome and its tRNA-exit region. Biochimie (2015) 0.75
The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics (2002) 29.41
Appion: an integrated, database-driven pipeline to facilitate EM image processing. J Struct Biol (2009) 5.71
RNAML: a standard syntax for exchanging RNA information. RNA (2002) 5.34
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat Struct Biol (2003) 3.77
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J (2002) 3.57
Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins. Cell (2003) 3.28
The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol (2002) 3.11
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement. Cell (2003) 3.03
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics (2004) 2.57
Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure (2008) 2.11
Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly. Mol Cell (2005) 1.93
The COPII cage: unifying principles of vesicle coat assembly. Nat Rev Mol Cell Biol (2006) 1.88
Investigation of viral DNA packaging using molecular mechanics models. Biophys Chem (2002) 1.65
Structural and thermodynamic principles of viral packaging. Structure (2007) 1.57
Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs. J Mol Biol (2004) 1.47
A structural model for the large subunit of the mammalian mitochondrial ribosome. J Mol Biol (2006) 1.46
ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae. Mol Phylogenet Evol (2003) 1.40
Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study. Biophys J (2006) 1.39
Structure of a mitochondrial ribosome with minimal RNA. Proc Natl Acad Sci U S A (2009) 1.38
Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM. Mol Cell (2005) 1.38
Packaging double-helical DNA into viral capsids: structures, forces, and energetics. Biophys J (2008) 1.37
Double belt structure of discoidal high density lipoproteins: molecular basis for size heterogeneity. J Mol Biol (2004) 1.36
Nodavirus coat protein imposes dodecahedral RNA structure independent of nucleotide sequence and length. J Virol (2004) 1.35
The lonepair triloop: a new motif in RNA structure. J Mol Biol (2003) 1.34
The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape. J Struct Biol (2007) 1.28
YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models. J Chem Theory Comput (2006) 1.27
Packaging of DNA by bacteriophage epsilon15: structure, forces, and thermodynamics. Structure (2007) 1.26
Packaging double-helical DNA into viral capsids. Biopolymers (2004) 1.22
Structural aspects of RbfA action during small ribosomal subunit assembly. Mol Cell (2007) 1.20
Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA. Int Conf Sci Stat Database Manag (2009) 1.20
Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Res (2013) 1.17
Structural and electrostatic characterization of pariacoto virus: implications for viral assembly. Biopolymers (2009) 1.15
A structural model for the assembly of the 30S subunit of the ribosome. J Mol Biol (2003) 1.14
New insights into the structural mechanisms of the COPII coat. Traffic (2009) 1.13
Placement of attine ant-associated Pseudonocardia in a global Pseudonocardia phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models. Antonie Van Leeuwenhoek (2010) 1.13
Monolithic microfluidic mixing-spraying devices for time-resolved cryo-electron microscopy. J Struct Biol (2009) 1.11
Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure. J Mol Biol (2011) 1.11
Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5 Å resolution. Structure (2012) 1.10
The origin and evolution of the ribosome. Biol Direct (2008) 1.10
DNA organization and thermodynamics during viral packing. Biophys J (2007) 1.09
Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20. Virology (2012) 1.09
Does linezolid cause lactic acidosis by inhibiting mitochondrial protein synthesis? Clin Infect Dis (2005) 1.08
Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits. Mol Cell (2007) 1.08
Molecular dynamics simulations on discoidal HDL particles suggest a mechanism for rotation in the apo A-I belt model. J Mol Biol (2002) 1.07
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins. Proc Natl Acad Sci U S A (2007) 1.07
Specificity between lactobacilli and hymenopteran hosts is the exception rather than the rule. Appl Environ Microbiol (2013) 1.06
YUP.SCX: coaxing atomic models into medium resolution electron density maps. J Struct Biol (2008) 1.06
A single mammalian mitochondrial translation initiation factor functionally replaces two bacterial factors. Mol Cell (2008) 1.06
RNA folding and catalysis mediated by iron (II). PLoS One (2012) 1.05
GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops. BMC Res Notes (2012) 1.05
Identification of the proteoglycan binding site in apolipoprotein B48. J Biol Chem (2002) 1.04
The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. PLoS One (2012) 1.04
A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry. Nat Struct Mol Biol (2012) 1.02
Creating an infrastructure for high-throughput high-resolution cryogenic electron microscopy. J Struct Biol (2012) 1.01
Isolation and characterization of mitochondrial ribosomes and ribosomal subunits from Leishmania tarentolae. Mol Biochem Parasitol (2006) 1.01
The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. J Mol Biol (2006) 1.01
Assembly of lipoprotein particles containing apolipoprotein-B: structural model for the nascent lipoprotein particle. Biophys J (2005) 1.00
PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G). J Biol Chem (2009) 0.99
Structural insights into initial and intermediate steps of the ribosome-recycling process. EMBO J (2012) 0.99
Comparative models for human apolipoprotein A-I bound to lipid in discoidal high-density lipoprotein particles. Biochemistry (2002) 0.99
Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B (2010) 0.98
Molecular dynamics simulations of forced unbending of integrin α(v)β₃. PLoS Comput Biol (2011) 0.95
Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding. RNA (2010) 0.95
Role of DNA-DNA interactions on the structure and thermodynamics of bacteriophages Lambda and P4. J Struct Biol (2010) 0.94
A model for the structure of satellite tobacco mosaic virus. J Struct Biol (2012) 0.94
The entropic cost of polymer confinement. J Phys Chem B (2012) 0.92
Probing the importance of tRNA anticodon: human immunodeficiency virus type 1 (HIV-1) RNA genome complementarity with an HIV-1 that selects tRNA(Glu) for replication. J Virol (2003) 0.92
Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae. Mol Biochem Parasitol (2007) 0.92
Modeling the conformational changes underlying channel opening in CFTR. PLoS One (2013) 0.92
Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding. J Mol Biol (2009) 0.91
The role of DNA twist in the packaging of viral genomes. Biophys J (2008) 0.91
RiboVision suite for visualization and analysis of ribosomes. Faraday Discuss (2014) 0.90
Structural constraints identified with covariation analysis in ribosomal RNA. PLoS One (2012) 0.88
In vitro secondary structure of the genomic RNA of satellite tobacco mosaic virus. PLoS One (2013) 0.87
Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state. RNA (2012) 0.87
The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny. Eur J Phycol (2009) 0.87
Biophysical and ultrastructural characterization of adeno-associated virus capsid uncoating and genome release. J Virol (2012) 0.87
Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1. Proc Natl Acad Sci U S A (2011) 0.86
Integration host factor (IHF) dictates the structure of polyamine-DNA condensates: implications for the role of IHF in the compaction of bacterial chromatin. Biochemistry (2009) 0.86
RNA with iron(II) as a cofactor catalyses electron transfer. Nat Chem (2013) 0.86
Biclustering as a method for RNA local multiple sequence alignment. Bioinformatics (2007) 0.86
The structure of the Sec13/31 COPII cage bound to Sec23. J Mol Biol (2012) 0.85
DNA-directed assembly of polyanilines: modified cytosine nucleotides transfer sequence programmability to a conjoined polymer. J Am Chem Soc (2006) 0.85
Molecular paleontology: a biochemical model of the ancestral ribosome. Nucleic Acids Res (2013) 0.84
Characterization of DNA conformation inside bacterial viruses. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.83
rCAD: A Novel Database Schema for the Comparative Analysis of RNA. Proc IEEE Int Conf Escience (2011) 0.82
RNA-magnesium-protein interactions in large ribosomal subunit. J Phys Chem B (2012) 0.82