Published in Nucleic Acids Res on July 01, 2005
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res (2014) 8.86
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods (2011) 6.06
Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. Proc Natl Acad Sci U S A (2007) 5.48
Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc (2009) 5.42
Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nat Struct Mol Biol (2011) 5.02
Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin. Proc Natl Acad Sci U S A (2009) 4.88
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14
Template-based protein structure modeling using the RaptorX web server. Nat Protoc (2012) 3.68
The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res (2006) 3.45
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J (2010) 3.40
I-TASSER: fully automated protein structure prediction in CASP8. Proteins (2009) 3.21
The fifth adaptor protein complex. PLoS Biol (2011) 2.94
A newly discovered protein export machine in malaria parasites. Nature (2009) 2.79
The Protein Model Portal--a comprehensive resource for protein structure and model information. Database (Oxford) (2013) 2.76
X-linked TEX11 mutations, meiotic arrest, and azoospermia in infertile men. N Engl J Med (2015) 2.71
Control of iron homeostasis by an iron-regulated ubiquitin ligase. Science (2009) 2.60
Structure of the TRPA1 ion channel suggests regulatory mechanisms. Nature (2015) 2.47
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol (2013) 2.44
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res (2013) 2.35
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Res (2008) 2.32
The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs. Bioinformatics (2013) 2.31
Structure and control of the actin regulatory WAVE complex. Nature (2010) 2.25
Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia. PLoS One (2011) 2.23
Proteasomal control of cytokinin synthesis protects Mycobacterium tuberculosis against nitric oxide. Mol Cell (2015) 2.18
High-throughput knockout screen in Schizosaccharomyces pombe identifies a novel gene required for efficient homolog disjunction during meiosis I. Cell Cycle (2010) 2.18
Cryo-EM structure of the DNA-dependent protein kinase catalytic subunit at subnanometer resolution reveals alpha helices and insight into DNA binding. Structure (2008) 2.17
Cell fate regulation governed by a repurposed bacterial histidine kinase. PLoS Biol (2014) 2.17
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics (2011) 2.13
Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease. Front Genet (2012) 2.08
A Distinct Type of Pilus from the Human Microbiome. Cell (2016) 2.05
Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct (2012) 2.05
Near-atomic resolution structural model of the yeast 26S proteasome. Proc Natl Acad Sci U S A (2012) 2.04
Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Nature (2012) 2.03
High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J Virol (2012) 2.03
Roles of pgaABCD genes in synthesis, modification, and export of the Escherichia coli biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine. J Bacteriol (2008) 2.02
Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Proc Natl Acad Sci U S A (2012) 1.99
High-resolution comparative modeling with RosettaCM. Structure (2013) 1.96
PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature (2013) 1.96
Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci U S A (2012) 1.96
Common ancestry of the CENP-A chaperones Scm3 and HJURP. Cell (2009) 1.96
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci U S A (2011) 1.96
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res (2010) 1.94
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
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. BMC Bioinformatics (2007) 1.89
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun (2014) 1.88
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea. Nature (2012) 1.86
De novo high-resolution protein structure determination from sparse spin-labeling EPR data. Structure (2008) 1.84
Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Nature (2015) 1.83
HHsenser: exhaustive transitive profile search using HMM-HMM comparison. Nucleic Acids Res (2006) 1.82
Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell (2010) 1.82
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics (2009) 1.80
Proteolytic elimination of N-myristoyl modifications by the Shigella virulence factor IpaJ. Nature (2013) 1.79
Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis. Sci Transl Med (2012) 1.78
Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration. PLoS Pathog (2006) 1.76
Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays (2011) 1.76
CASP9 target classification. Proteins (2011) 1.75
Structure of the CRISPR interference complex CSM reveals key similarities with cascade. Mol Cell (2013) 1.74
WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes. Proc Natl Acad Sci U S A (2010) 1.71
A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations. Nat Genet (2013) 1.70
A thiolase of Mycobacterium tuberculosis is required for virulence and production of androstenedione and androstadienedione from cholesterol. Infect Immun (2009) 1.69
Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc Natl Acad Sci U S A (2008) 1.68
Structural basis for gating charge movement in the voltage sensor of a sodium channel. Proc Natl Acad Sci U S A (2011) 1.68
The complex that inserts lipopolysaccharide into the bacterial outer membrane forms a two-protein plug-and-barrel. Proc Natl Acad Sci U S A (2011) 1.68
Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion. Nature (2014) 1.68
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
Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre. Mol Microbiol (2013) 1.67
Derlin-1 is a rhomboid pseudoprotease required for the dislocation of mutant α-1 antitrypsin from the endoplasmic reticulum. Nat Struct Mol Biol (2011) 1.64
Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination. Biol Direct (2008) 1.61
Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med (2015) 1.60
Architecture of mammalian respiratory complex I. Nature (2014) 1.60
Structural insight into epitopes in the pregnancy-associated malaria protein VAR2CSA. PLoS Pathog (2008) 1.60
Early-arriving Syp1p and Ede1p function in endocytic site placement and formation in budding yeast. Mol Biol Cell (2009) 1.60
I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res (2015) 1.59
Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds. Proc Natl Acad Sci U S A (2008) 1.59
A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J (2011) 1.58
Characterization of the Newly Isolated Lytic Bacteriophages KTN6 and KT28 and Their Efficacy against Pseudomonas aeruginosa Biofilm. PLoS One (2015) 1.58
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct (2009) 1.58
A novel pathway of intercellular signalling in Bacillus subtilis involves a protein with similarity to a component of type III secretion channels. Mol Microbiol (2008) 1.58
CENP-T proteins are conserved centromere receptors of the Ndc80 complex. Nat Cell Biol (2012) 1.55
Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex. EMBO J (2009) 1.55
Architecture and function of IFT complex proteins in ciliogenesis. Differentiation (2011) 1.55
Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol (2011) 1.53
FFAS server: novel features and applications. Nucleic Acids Res (2011) 1.52
T4-related bacteriophage LIMEstone isolates for the control of soft rot on potato caused by 'Dickeya solani'. PLoS One (2012) 1.52
Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity. J Virol (2008) 1.52
Caenorhabditis elegans HIM-18/SLX-4 interacts with SLX-1 and XPF-1 and maintains genomic integrity in the germline by processing recombination intermediates. PLoS Genet (2009) 1.52
Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. Nat Commun (2016) 1.49
A channel connecting the mother cell and forespore during bacterial endospore formation. Proc Natl Acad Sci U S A (2008) 1.49
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res (2008) 1.49
Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening. Nat Struct Mol Biol (2012) 1.48
Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature (2015) 1.47
Evidence for a novel protease governing regulated intramembrane proteolysis and resistance to antimicrobial peptides in Bacillus subtilis. Genes Dev (2006) 1.47
Drosophila TIM binds importin α1, and acts as an adapter to transport PER to the nucleus. PLoS Genet (2015) 1.46
Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. PLoS Comput Biol (2016) 1.46
MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes. PLoS Biol (2013) 1.45
Previously unknown and highly divergent ssDNA viruses populate the oceans. ISME J (2013) 1.44
Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. J Biol Chem (2010) 1.44
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Profile hidden Markov models. Bioinformatics (1998) 56.04
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
Protein homology detection by HMM-HMM comparison. Bioinformatics (2004) 21.92
CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res (2002) 18.54
SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res (1999) 11.33
Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics (1991) 9.65
Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res (1998) 8.87
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol (2003) 8.35
3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res (2004) 7.03
Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol (2001) 6.63
Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res (1996) 5.68
Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol (2002) 4.99
Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell (2003) 3.66
Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc Natl Acad Sci U S A (2004) 3.63
Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes. Nucleic Acids Res (2000) 3.16
3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins (2003) 2.91
CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60
Evolution of protein structures and functions. Curr Opin Struct Biol (2002) 2.38
Fold and function predictions for Mycoplasma genitalium proteins. Fold Des (1998) 2.02
Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res (2003) 1.88
Profile-profile alignment: a powerful tool for protein structure prediction. Pac Symp Biocomput (2003) 1.76
Expression of AbrB, a transition state regulator from Bacillus subtilis, is growth phase dependent in a manner resembling that of Fis, the nucleoid binding protein from Escherichia coli. J Bacteriol (1997) 1.61
Sensitive sequence comparison as protein function predictor. Pac Symp Biocomput (2000) 1.57
DNA-binding studies on the Bacillus subtilis transcriptional regulator and AbrB homologue, SpoVT. FEMS Microbiol Lett (2004) 1.43
Protein structure prediction for the male-specific region of the human Y chromosome. Proc Natl Acad Sci U S A (2004) 1.43
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins (2004) 1.41
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
Protein domain of unknown function DUF1023 is an alpha/beta hydrolase. Proteins (2005) 1.23
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods (2011) 6.06
The HAMP domain structure implies helix rotation in transmembrane signaling. Cell (2006) 4.34
The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res (2006) 3.45
Fast and accurate automatic structure prediction with HHpred. Proteins (2009) 2.98
PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res (2004) 2.26
Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases. Mol Cell (2009) 2.05
Phylogenetic analysis of AAA proteins. J Struct Biol (2004) 1.92
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. BMC Bioinformatics (2007) 1.89
More than the sum of their parts: on the evolution of proteins from peptides. Bioessays (2003) 1.83
HHsenser: exhaustive transitive profile search using HMM-HMM comparison. Nucleic Acids Res (2006) 1.82
prlF and yhaV encode a new toxin-antitoxin system in Escherichia coli. J Mol Biol (2007) 1.57
Classification of AAA+ proteins. J Struct Biol (2006) 1.55
REPPER--repeats and their periodicities in fibrous proteins. Nucleic Acids Res (2005) 1.50
Evolution of the beta-propeller fold. Proteins (2008) 1.48
Modeling AAA+ ring complexes from monomeric structures. J Struct Biol (2006) 1.48
AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels. Structure (2005) 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
Comparative analysis of coiled-coil prediction methods. J Struct Biol (2006) 1.43
Comprehensive analysis of HAMP domains: implications for transmembrane signal transduction. J Mol Biol (2010) 1.35
HHrep: de novo protein repeat detection and the origin of TIM barrels. Nucleic Acids Res (2006) 1.32
The mechanisms of HAMP-mediated signaling in transmembrane receptors. Structure (2011) 1.30
Historical review: another 50th anniversary--new periodicities in coiled coils. Trends Biochem Sci (2003) 1.29
Gene duplication of the eight-stranded beta-barrel OmpX produces a functional pore: a scenario for the evolution of transmembrane beta-barrels. J Mol Biol (2006) 1.22
Model structure of the prototypical non-fimbrial adhesin YadA of Yersinia enterocolitica. J Struct Biol (2006) 1.20
A polycystin-2 (TRPP2) dimerization domain essential for the function of heteromeric polycystin complexes. EMBO J (2010) 1.18
Structure of the head of the Bartonella adhesin BadA. PLoS Pathog (2008) 1.17
HHomp--prediction and classification of outer membrane proteins. Nucleic Acids Res (2009) 1.16
Mechanism of regulation of receptor histidine kinases. Structure (2012) 1.13
Purification of the YadA membrane anchor for secondary structure analysis and crystallization. Int J Biol Macromol (2006) 1.09
Evolutionary relationships of microbial aromatic prenyltransferases. PLoS One (2011) 1.09
A conserved glycine residue of trimeric autotransporter domains plays a key role in Yersinia adhesin A autotransport. J Bacteriol (2007) 1.08
SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay. Genes Dev (2010) 1.08
Cradle-loop barrels and the concept of metafolds in protein classification by natural descent. Curr Opin Struct Biol (2008) 1.07
The Sulfolobus solfataricus AAA protein Sso0909, a homologue of the eukaryotic ESCRT Vps4 ATPase. Biochem Soc Trans (2008) 1.07
A coiled-coil motif that sequesters ions to the hydrophobic core. Proc Natl Acad Sci U S A (2009) 1.07
Common evolutionary origin of swapped-hairpin and double-psi beta barrels. Structure (2006) 1.06
A galaxy of folds. Protein Sci (2010) 1.05
The head of Bartonella adhesin A is crucial for host cell interaction of Bartonella henselae. Cell Microbiol (2008) 1.01
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bioinformatics (2008) 1.00
On the origin of the histone fold. BMC Struct Biol (2007) 1.00
Functional mapping of YadA- and Ail-mediated binding of human factor H to Yersinia enterocolitica serotype O:3. Infect Immun (2008) 0.99
Coiled coils meet the chaperone world. Trends Biochem Sci (2004) 0.98
Discriminative modelling of context-specific amino acid substitution probabilities. Bioinformatics (2012) 0.98
A new expression system for protein crystallization using trimeric coiled-coil adaptors. Protein Eng Des Sel (2007) 0.98
The structure of E. coli IgG-binding protein D suggests a general model for bending and binding in trimeric autotransporter adhesins. Structure (2011) 0.95
Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria. Proc Natl Acad Sci U S A (2012) 0.95
Bioinformatics of the TULIP domain superfamily. Biochem Soc Trans (2011) 0.93
A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins. J Struct Biol (2010) 0.91
Crystal structure of SpoVT, the final modulator of gene expression during spore development in Bacillus subtilis. J Mol Biol (2008) 0.90
β-Propeller blades as ancestral peptides in protein evolution. PLoS One (2013) 0.88
Fold recognition without folds. Protein Sci (2002) 0.88
Measuring the conformational space of square four-helical bundles with the program samCC. J Struct Biol (2010) 0.88
Structure and function of tripeptidyl peptidase II, a giant cytosolic protease. Biochim Biophys Acta (2011) 0.87
A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Structure (2007) 0.87
Crystal structure of a dimeric archaeal cleavage and polyadenylation specificity factor. J Struct Biol (2010) 0.86
The archaeal proteasome is regulated by a network of AAA ATPases. J Biol Chem (2012) 0.86
Inherent chaperone-like activity of aspartic proteases reveals a distant evolutionary relation to double-psi barrel domains of AAA-ATPases. Protein Sci (2007) 0.83
The first prokaryotic trehalose synthase complex identified in the hyperthermophilic crenarchaeon Thermoproteus tenax. PLoS One (2013) 0.81
The GD box: a widespread noncontiguous supersecondary structural element. Protein Sci (2009) 0.81
The use of FLP-mediated recombination for the functional analysis of an effector gene family in the biotrophic smut fungus Ustilago maydis. New Phytol (2010) 0.80
PDBalert: automatic, recurrent remote homology tracking and protein structure prediction. BMC Struct Biol (2008) 0.78
Characterization of AMA, a new AAA protein from Archaeoglobus and methanogenic archaea. J Struct Biol (2006) 0.77
Two unique membrane-bound AAA proteins from Sulfolobus solfataricus. Biochem Soc Trans (2009) 0.76
The structure of proteins. J Struct Biol (2012) 0.75