Published in BMC Genomics on April 28, 2006
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Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics (2007) 1.74
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The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection. Nucleic Acids Res (2009) 1.21
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Mobile DNA elements in T4 and related phages. Virol J (2010) 1.11
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI. Structure (2010) 1.11
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Scientific serendipity initiates an intron odyssey. J Biol Chem (2009) 0.99
The endonuclease Ankle1 requires its LEM and GIY-YIG motifs for DNA cleavage in vivo. J Cell Sci (2012) 0.97
Resolving branched DNA intermediates with structure-specific nucleases during replication in eukaryotes. Chromosoma (2013) 0.95
An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI. Nucleic Acids Res (2009) 0.95
LEM-3 - A LEM domain containing nuclease involved in the DNA damage response in C. elegans. PLoS One (2012) 0.94
Holliday junction resolvases. Cold Spring Harb Perspect Biol (2014) 0.94
Insights into bacteriophage T5 structure from analysis of its morphogenesis genes and protein components. J Virol (2013) 0.91
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Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements. Mob DNA (2013) 0.87
Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family. Nucleic Acids Res (2007) 0.87
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Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI. PLoS One (2011) 0.85
Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis. J Bacteriol (2008) 0.82
Structural insights into the N-terminal GIY-YIG endonuclease activity of Arabidopsis glutaredoxin AtGRXS16 in chloroplasts. Proc Natl Acad Sci U S A (2013) 0.82
The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA. Nucleic Acids Res (2013) 0.81
Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group. Nucleic Acids Res (2007) 0.80
The SMX DNA Repair Tri-nuclease. Mol Cell (2017) 0.79
The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land. Sci Rep (2016) 0.79
Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families. Mob DNA (2013) 0.78
Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the H-N-H and GIY-YIG motifs. Nucleic Acids Res (2009) 0.78
Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease. Cell Rep (2015) 0.78
Bacteriophage T4 endonuclease II, a promiscuous GIY-YIG nuclease, binds as a tetramer to two DNA substrates. Nucleic Acids Res (2009) 0.78
Fusion of a superfamily 1 helicase and an inactivated DNA polymerase is a signature of common evolutionary history of Polintons, polinton-like viruses, Tlr1 transposons and transpovirons. Virus Evol (2016) 0.77
The GIY-YIG Type Endonuclease Ankyrin Repeat and LEM Domain-Containing Protein 1 (ANKLE1) Is Dispensable for Mouse Hematopoiesis. PLoS One (2016) 0.76
Whole genome sequences of three Clade 3 Clostridium difficile strains carrying binary toxin genes in China. Sci Rep (2017) 0.75
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. BMC Bioinformatics (2015) 0.75
Trends in genome dynamics among major orders of insects revealed through variations in protein families. BMC Genomics (2015) 0.75
Resolvase OsGEN1 mediates DNA repair by homologous recombination. Plant Physiol (2017) 0.75
The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts. BMC Genomics (2015) 0.75
Nucleo-cytoplasmic shuttling of the endonuclease ankyrin repeats and LEM domain-containing protein 1 (Ankle1) is mediated by canonical nuclear export- and nuclear import signals. BMC Cell Biol (2016) 0.75
Comprehensive classification of the PIN domain-like superfamily. Nucleic Acids Res (2017) 0.75
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InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
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Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol (2000) 10.87
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol (2001) 10.02
GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol (1999) 6.42
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Genome evolution in bacterial endosymbionts of insects. Nat Rev Genet (2002) 4.16
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SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res (2000) 3.56
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Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci (2001) 2.90
The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol (2001) 2.84
Mutations in the RNA polymerase II transcription machinery suppress the hyperrecombination mutant hpr1 delta of Saccharomyces cerevisiae. Genetics (1996) 2.74
Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins (2003) 2.67
A phylogenomic study of the MutS family of proteins. Nucleic Acids Res (1998) 2.54
Accurate prediction of solvent accessibility using neural networks-based regression. Proteins (2004) 2.54
Slx1-Slx4 is a second structure-specific endonuclease functionally redundant with Sgs1-Top3. Genes Dev (2003) 2.53
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
Nucleotide excision repair. Prog Nucleic Acid Res Mol Biol (2005) 2.31
Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput (2000) 2.28
Unusual life style of giant chlorella viruses. Annu Rev Genet (2003) 2.22
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res (2001) 2.19
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins (2004) 2.16
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Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Mol Biol Cell (2003) 1.96
SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. J Mol Microbiol Biotechnol (2002) 1.95
Mutations at the Arabidopsis CHM locus promote rearrangements of the mitochondrial genome. Plant Cell (1992) 1.91
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Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Mol Biol Cell (2005) 1.66
Guilt by association: contextual information in genome analysis. Genome Res (2000) 1.65
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Catalytic sites for 3' and 5' incision of Escherichia coli nucleotide excision repair are both located in UvrC. J Biol Chem (2000) 1.51
Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns. Genes Dev (2002) 1.51
Altered mitochondrial gene expression in a maternal distorted leaf mutant of Arabidopsis induced by chloroplast mutator. Plant Cell (1996) 1.48
The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol Biol Evol (2005) 1.46
Solution structure of the constant region of nuclear envelope protein LAP2 reveals two LEM-domain structures: one binds BAF and the other binds DNA. EMBO J (2001) 1.42
Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation. In Silico Biol (2001) 1.42
A novel family of mobile genetic elements is limited to the germline genome in Tetrahymena thermophila. Nucleic Acids Res (2002) 1.41
Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Nat Struct Biol (2002) 1.41
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Genome Biol (2002) 1.34
Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate. EMBO J (2001) 1.32
Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology. Curr Protein Pept Sci (2003) 1.30
Structural insights into the first incision reaction during nucleotide excision repair. EMBO J (2005) 1.30
Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. Trends Biochem Sci (2001) 1.25
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Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J Mol Evol (2000) 1.21
A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective. Res Microbiol (2005) 1.18
Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair. Proc Natl Acad Sci U S A (2002) 1.15
New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Trends Biochem Sci (2003) 1.11
Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs. Genes Cells (2002) 1.10
Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements. Proc Natl Acad Sci U S A (2004) 1.08
The structure and evolution of Penelope in the virilis species group of Drosophila: an ancient lineage of retroelements. J Mol Evol (2001) 1.01
Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli. EMBO J (2002) 1.00
A cut above: discovery of an alternative excision repair pathway in bacteria. Proc Natl Acad Sci U S A (2002) 0.99
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
In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments. J Virol (1983) 0.97
All in the family: evidence for four new LEM-domain proteins Lem2 (NET-25), Lem3, Lem4 and Lem5 in the human genome. Symp Soc Exp Biol (2004) 0.96
Homing endonucleases encoded by germ line-limited genes in Tetrahymena thermophila have APETELA2 DNA binding domains. Eukaryot Cell (2004) 0.93
Thermus thermophilus MutS2, a MutS paralogue, possesses an endonuclease activity promoted by MutL. J Biochem (2004) 0.92
Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases. Protein Sci (2001) 0.85
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics. Protein Eng (2001) 0.82
MODOMICS: a database of RNA modification pathways--2013 update. Nucleic Acids Res (2012) 4.43
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Transcriptome profile of human colorectal adenomas. Mol Cancer Res (2007) 3.82
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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
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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
Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m(6)A methyltransferase. J Mol Evol (2002) 1.68
Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J (2002) 1.66
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
Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases. Nucleic Acids Res (2004) 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
Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. J Mol Biol (2007) 1.18
The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase. J Bacteriol (2003) 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
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. BMC Bioinformatics (2011) 1.15
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA (2008) 1.15
MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase. EMBO J (2002) 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
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
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
Complete cap 4 formation is not required for viability in Trypanosoma brucei. Eukaryot Cell (2006) 1.00
SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes. Genes Dev (2009) 0.99
Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease. Proteins (2006) 0.99
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
New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Nucleic Acids Res (2010) 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
RNA Bricks--a database of RNA 3D motifs and their interactions. Nucleic Acids Res (2013) 0.98
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res (2013) 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
REPAIRtoire--a database of DNA repair pathways. Nucleic Acids Res (2010) 0.97
Distribution and frequencies of post-transcriptional modifications in tRNAs. RNA Biol (2014) 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
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