Published in Bioinformatics on July 29, 2004
The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res (2006) 3.45
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One (2009) 3.03
The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs. Bioinformatics (2013) 2.31
Fido, a novel AMPylation domain common to fic, doc, and AvrB. PLoS One (2009) 1.92
Uncovering the human methyltransferasome. Mol Cell Proteomics (2010) 1.91
HHsenser: exhaustive transitive profile search using HMM-HMM comparison. Nucleic Acids Res (2006) 1.82
A survey of visualization tools for biological network analysis. BioData Min (2008) 1.76
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics (2007) 1.74
Bioinformatic analysis of the CLE signaling peptide family. BMC Plant Biol (2008) 1.66
Phylogenomic analysis of the GIY-YIG nuclease superfamily. BMC Genomics (2006) 1.56
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res (2008) 1.49
A novel plant gene essential for meiosis is related to the human CtIP and the yeast COM1/SAE2 gene. EMBO J (2007) 1.46
De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nat Chem Biol (2015) 1.45
Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria. Bioinformatics (2010) 1.44
Discovery of an archetypal protein transport system in bacterial outer membranes. Nat Struct Mol Biol (2012) 1.41
Allosteric regulation of Argonaute proteins by miRNAs. Nat Struct Mol Biol (2010) 1.40
Isolation and characterisation of KP34--a novel φKMV-like bacteriophage for Klebsiella pneumoniae. Appl Microbiol Biotechnol (2011) 1.30
Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput Biol (2012) 1.29
Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. BMC Bioinformatics (2005) 1.29
Global view of the evolution and diversity of metazoan neuropeptide signaling. Proc Natl Acad Sci U S A (2013) 1.24
Discrete-continuous duality of protein structure space. Curr Opin Struct Biol (2009) 1.24
Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis. BMC Biol (2012) 1.21
Distribution and functions of TonB-dependent transporters in marine bacteria and environments: implications for dissolved organic matter utilization. PLoS One (2012) 1.21
Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. PLoS Genet (2011) 1.20
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res (2012) 1.18
The origins of specificity in polyketide synthase protein interactions. PLoS Comput Biol (2007) 1.18
Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J Biol Chem (2007) 1.17
Inference of functional properties from large-scale analysis of enzyme superfamilies. J Biol Chem (2011) 1.17
HHomp--prediction and classification of outer membrane proteins. Nucleic Acids Res (2009) 1.16
Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family. BMC Genomics (2008) 1.15
On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2. PLoS One (2011) 1.13
CREST--a large and diverse superfamily of putative transmembrane hydrolases. Biol Direct (2011) 1.12
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol (2006) 1.12
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res (2016) 1.10
Evolutionary relationships of microbial aromatic prenyltransferases. PLoS One (2011) 1.09
A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes. PLoS One (2012) 1.08
Omp85 from the thermophilic cyanobacterium Thermosynechococcus elongatus differs from proteobacterial Omp85 in structure and domain composition. J Biol Chem (2010) 1.07
Marker for type VI secretion system effectors. Proc Natl Acad Sci U S A (2014) 1.06
A galaxy of folds. Protein Sci (2010) 1.05
Recurrent horizontal transfer of bacterial toxin genes to eukaryotes. Mol Biol Evol (2012) 1.05
The essentials of protein import in the degenerate mitochondrion of Entamoeba histolytica. PLoS Pathog (2010) 1.05
Structural and functional insight into the universal stress protein family. Evol Appl (2013) 1.05
TonB-dependent transporters and their occurrence in cyanobacteria. BMC Biol (2009) 1.04
A novel metal transporter mediating manganese export (MntX) regulates the Mn to Fe intracellular ratio and Neisseria meningitidis virulence. PLoS Pathog (2011) 1.04
Structural and immunologic characterization of Ara h 1, a major peanut allergen. J Biol Chem (2011) 1.03
Domain shuffling in a sensor protein contributed to the evolution of insect pathogenicity in plant-beneficial Pseudomonas protegens. PLoS Pathog (2014) 1.03
The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators. Nucleic Acids Res (2009) 1.03
The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif. Biol Direct (2009) 1.02
TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog. Dev Comp Immunol (2010) 1.01
The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode. Plant Cell (2008) 1.00
LTR retrotransposons in fungi. PLoS One (2011) 1.00
Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics (2014) 1.00
Assembly of the type II secretion system such as found in Vibrio cholerae depends on the novel Pilotin AspS. PLoS Pathog (2013) 0.98
A systematic investigation of multiheme c-type cytochromes in prokaryotes. J Biol Inorg Chem (2010) 0.98
A tethered delivery mechanism explains the catalytic action of a microtubule polymerase. Elife (2014) 0.98
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. BMC Genomics (2009) 0.98
Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1. J Mol Biol (2011) 0.97
Structural bioinformatics of the human spliceosomal proteome. Nucleic Acids Res (2012) 0.96
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. Nucleic Acids Res (2006) 0.96
The protein import channel in the outer mitosomal membrane of Giardia intestinalis. Mol Biol Evol (2009) 0.96
Improving Hox protein classification across the major model organisms. PLoS One (2010) 0.96
Mitochondrial sorting and assembly machinery subunit Sam37 in Candida albicans: insight into the roles of mitochondria in fitness, cell wall integrity, and virulence. Eukaryot Cell (2012) 0.95
Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein. PLoS One (2007) 0.95
2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. Nucleic Acids Res (2011) 0.94
Structure of signal-regulatory protein alpha: a link to antigen receptor evolution. J Biol Chem (2009) 0.94
WXG100 protein superfamily consists of three subfamilies and exhibits an α-helical C-terminal conserved residue pattern. PLoS One (2014) 0.94
Structural and functional analysis of the MutS C-terminal tetramerization domain. Nucleic Acids Res (2006) 0.93
Independent subtilases expansions in fungi associated with animals. Mol Biol Evol (2011) 0.93
Genome-wide analysis of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network. PLoS One (2011) 0.93
PCOPGene-Net: holistic characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships. BMC Bioinformatics (2009) 0.92
The evolution of microRNA pathway protein components in Cnidaria. Mol Biol Evol (2013) 0.92
Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res (2013) 0.91
Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting. Appl Environ Microbiol (2009) 0.91
SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. Nucleic Acids Res (2013) 0.91
The discovery of phiAGATE, a novel phage infecting Bacillus pumilus, leads to new insights into the phylogeny of the subfamily Spounavirinae. PLoS One (2014) 0.90
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. Nucleic Acids Res (2014) 0.90
The neuropeptide complement of the marine annelid Platynereis dumerilii. BMC Genomics (2013) 0.90
Citrate sensing by the C4-dicarboxylate/citrate sensor kinase DcuS of Escherichia coli: binding site and conversion of DcuS to a C4-dicarboxylate- or citrate-specific sensor. J Bacteriol (2007) 0.90
Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. Trends Microbiol (2016) 0.89
Rhodococcus sp. strain CR-53 LipR, the first member of a new bacterial lipase family (family X) displaying an unusual Y-type oxyanion hole, similar to the Candida antarctica lipase clan. Appl Environ Microbiol (2012) 0.89
Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison. New Phytol (2012) 0.88
β-Propeller blades as ancestral peptides in protein evolution. PLoS One (2013) 0.88
Evidence for an evolutionary antagonism between Mrr and Type III modification systems. Nucleic Acids Res (2011) 0.88
From cyanobacteria to plants: conservation of PII functions during plastid evolution. Planta (2012) 0.88
Crystal structure of the human sterol transporter ABCG5/ABCG8. Nature (2016) 0.87
A novel predicted calcium-regulated kinase family implicated in neurological disorders. PLoS One (2013) 0.86
Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not? BMC Genomics (2012) 0.86
cor, a novel carbon monoxide resistance gene, is essential for Mycobacterium tuberculosis pathogenesis. MBio (2013) 0.86
Phylogenetic investigation of Peptide hormone and growth factor receptors in five dipteran genomes. Front Endocrinol (Lausanne) (2013) 0.86
Contrasting patterns of transposable element and satellite distribution on sex chromosomes (XY1Y2) in the dioecious plant Rumex acetosa. Genome Biol Evol (2013) 0.86
A new arylsulfate sulfotransferase involved in liponucleoside antibiotic biosynthesis in streptomycetes. J Biol Chem (2010) 0.86
Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size. Nucleic Acids Res (2011) 0.86
Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria. PLoS Pathog (2015) 0.86
The archaeal proteasome is regulated by a network of AAA ATPases. J Biol Chem (2012) 0.86
Conserved structure and inferred evolutionary history of long terminal repeats (LTRs). Mob DNA (2013) 0.85
Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. Bioinform Biol Insights (2012) 0.85
Family size evolution in Drosophila chemosensory gene families: a comparative analysis with a critical appraisal of methods. Genome Biol Evol (2014) 0.85
A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis. Plant Physiol (2015) 0.85
Biochemical characterization of a novel haloalkane dehalogenase from a cold-adapted bacterium. Appl Environ Microbiol (2012) 0.85
A bioinformatic survey of distribution, conservation, and probable functions of LuxR solo regulators in bacteria. Front Cell Infect Microbiol (2015) 0.85
WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy. Oncogene (2004) 2.86
Trimeric autotransporter adhesins: variable structure, common function. Trends Microbiol (2006) 2.02
Bartonella adhesin a mediates a proangiogenic host cell response. J Exp Med (2004) 1.84
Domain annotation of trimeric autotransporter adhesins--daTAA. Bioinformatics (2008) 1.41
Salmonella Pathogenicity Island 4 encodes a giant non-fimbrial adhesin and the cognate type 1 secretion system. Cell Microbiol (2007) 1.39
Barentsz, a new component of the Staufen-containing ribonucleoprotein particles in mammalian cells, interacts with Staufen in an RNA-dependent manner. J Neurosci (2003) 1.25
HAMP domain-mediated signal transduction probed with a mycobacterial adenylyl cyclase as a reporter. J Biol Chem (2011) 0.92
Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun (2006) 0.88
A trimeric lipoprotein assists in trimeric autotransporter biogenesis in enterobacteria. J Biol Chem (2013) 0.76
Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII. Nucleic Acids Res (2012) 0.75
Thermoplasma acidophilum TAA43 is an archaeal member of the eukaryotic meiotic branch of AAA ATPases. Biol Chem (2004) 0.75