Published in Nucleic Acids Res on November 15, 2012
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic Acids Res (2012) 1.66
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res (2011) 30.20
Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res (2011) 18.50
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res (2010) 6.58
Eukaryotic mRNA decapping. Annu Rev Biochem (2004) 6.35
RNA processing and its regulation: global insights into biological networks. Nat Rev Genet (2010) 5.34
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res (2011) 5.34
The many pathways of RNA degradation. Cell (2009) 5.31
Making ribosomes. Curr Opin Cell Biol (2002) 5.20
WikiPathways: building research communities on biological pathways. Nucleic Acids Res (2011) 4.78
BRENDA, the enzyme information system in 2011. Nucleic Acids Res (2010) 3.83
MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res (2008) 2.84
Subcellular mRNA localization in animal cells and why it matters. Science (2009) 2.54
The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev (2010) 2.31
RNA nucleotide methylation. Wiley Interdiscip Rev RNA (2011) 2.15
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
Biogenesis of mRNPs: integrating different processes in the eukaryotic nucleus. Chromosoma (2008) 1.69
Regulation of mRNP dynamics along the export pathway. FEBS Lett (2008) 1.43
mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem. IUBMB Life (2004) 1.38
Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression. Wiley Interdiscip Rev RNA (2010) 1.29
RNA processing and export. Cold Spring Harb Perspect Biol (2010) 1.22
Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism. RNA (2010) 1.20
REPAIRtoire--a database of DNA repair pathways. Nucleic Acids Res (2010) 0.97
Structural bioinformatics of the human spliceosomal proteome. Nucleic Acids Res (2012) 0.96
A complex 'mRNA degradation code' controls gene expression during animal development. Trends Genet (2012) 0.95
Crosstalk between RNA metabolic pathways: an RNOMICS approach. Nat Rev Mol Cell Biol (2005) 0.86
MODOMICS: a database of RNA modification pathways--2013 update. Nucleic Acids Res (2012) 4.43
GeneSilico protein structure prediction meta-server. Nucleic Acids Res (2003) 3.98
Transcriptome profile of human colorectal adenomas. Mol Cancer Res (2007) 3.82
MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res (2008) 2.84
A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins (2003) 2.39
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB. BMC Genomics (2003) 2.23
IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis. Nat Cell Biol (2008) 1.97
Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices. J Biol Chem (2002) 1.95
MODOMICS: a database of RNA modification pathways. Nucleic Acids Res (2006) 1.95
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics (2008) 1.88
ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res (2011) 1.85
Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains. J Biol Chem (2005) 1.75
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics (2007) 1.74
Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucleic Acids Res (2004) 1.73
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res (2003) 1.71
Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa. Mol Cell (2007) 1.70
Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J (2002) 1.66
Phylogenomic analysis of the GIY-YIG nuclease superfamily. BMC Genomics (2006) 1.56
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins (2005) 1.54
Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases. Gene (2003) 1.54
COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res (2004) 1.53
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res (2008) 1.49
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics (2012) 1.46
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. BMC Bioinformatics (2005) 1.46
The YTH domain is a novel RNA binding domain. J Biol Chem (2010) 1.45
A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res (2004) 1.44
Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII. Nucleic Acids Res (2005) 1.39
Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria. Nucleic Acids Res (2009) 1.38
Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits. Mol Cell Biol (2008) 1.38
The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res (2008) 1.37
Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res (2003) 1.35
Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA. Mol Cell Biol (2005) 1.35
N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota. J Biol Chem (2004) 1.34
Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase. Mol Cell (2009) 1.32
Analysis of the quaternary structure of the MutL C-terminal domain. J Mol Biol (2005) 1.30
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol Microbiol (2009) 1.30
FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6. Proteins (2005) 1.30
Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis. J Mol Biol (2004) 1.29
YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. J Mol Biol (2008) 1.26
Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res (2007) 1.22
The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol. J Biol Chem (2005) 1.19
RNA and protein 3D structure modeling: similarities and differences. J Mol Model (2011) 1.19
The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase. J Bacteriol (2003) 1.18
Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. J Mol Biol (2007) 1.18
Computational methods for prediction of protein-RNA interactions. J Struct Biol (2011) 1.17
Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase. Nucleic Acids Res (2003) 1.17
MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase. EMBO J (2002) 1.15
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA (2008) 1.15
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. BMC Bioinformatics (2011) 1.15
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. BMC Struct Biol (2007) 1.15
Integrating ELF4 into the circadian system through combined structural and functional studies. HFSP J (2009) 1.13
EXOG, a novel paralog of Endonuclease G in higher eukaryotes. Nucleic Acids Res (2008) 1.13
Structure and operation of the DNA-translocating type I DNA restriction enzymes. Genes Dev (2012) 1.13
Phylogenetic analysis of haloalkane dehalogenases. Proteins (2007) 1.12
Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases. Genome Biol (2008) 1.12
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol (2006) 1.12
Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res (2007) 1.11
Evolutionary relationship between different subgroups of restriction endonucleases. J Biol Chem (2002) 1.11
Binding of the low-density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes. Mol Microbiol (2006) 1.10
Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for malaria and leishmaniasis. J Biomed Sci (2002) 1.09
The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol (2008) 1.08
A toolbox for developing bioinformatics software. Brief Bioinform (2011) 1.06
THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain. Nucleic Acids Res (2006) 1.04
Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res (2011) 1.04
Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases. Nucleic Acids Res (2010) 1.04
Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. Nucleic Acids Res (2005) 1.03
Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J Mol Biol (2008) 1.02
ModeRNA server: an online tool for modeling RNA 3D structures. Bioinformatics (2011) 1.02
Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair. Hum Mutat (2010) 1.02
Cooperative binding of the hnRNP K three KH domains to mRNA targets. FEBS Lett (2004) 1.01
STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNγ, TLR4 and IL-6 in vascular disease. Cytokine Growth Factor Rev (2011) 1.01
Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences. J Biol Chem (2004) 1.01
The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode. Plant Cell (2008) 1.00
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol Biol (2006) 1.00
HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling. J Mol Biol (2007) 1.00
Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding. Nucleic Acids Res (2007) 1.00
Complete cap 4 formation is not required for viability in Trypanosoma brucei. Eukaryot Cell (2006) 1.00
Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions. Nucleic Acids Res (2003) 0.99
Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease. Proteins (2006) 0.99
SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes. Genes Dev (2009) 0.99
New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Nucleic Acids Res (2010) 0.98
RNA Bricks--a database of RNA 3D motifs and their interactions. Nucleic Acids Res (2013) 0.98
Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria. Microbiology (2005) 0.98
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res (2013) 0.97
Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'. J Mol Biol (2003) 0.97
Distribution and frequencies of post-transcriptional modifications in tRNAs. RNA Biol (2014) 0.97
REPAIRtoire--a database of DNA repair pathways. Nucleic Acids Res (2010) 0.97
Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes. Appl Environ Microbiol (2008) 0.97
Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA. Nucleic Acids Res (2006) 0.97
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. BMC Genomics (2005) 0.97
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition. Bioinformatics (2007) 0.97
Structural bioinformatics of the human spliceosomal proteome. Nucleic Acids Res (2012) 0.96
Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA. Proteins (2008) 0.96