Published in Nucleic Acids Res on February 19, 2008
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Quasi-consensus-based comparison of profile hidden Markov models for protein sequences. Bioinformatics (2005) 1.02
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Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell (2006) 11.38
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PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 7.16
Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell (2012) 6.83
Identification of the acyltransferase that octanoylates ghrelin, an appetite-stimulating peptide hormone. Cell (2008) 5.10
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics (2008) 4.36
Structural classification of zinc fingers: survey and summary. Nucleic Acids Res (2003) 3.94
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Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins (2009) 3.64
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
AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling. Science (2008) 3.44
A sequence variation (I148M) in PNPLA3 associated with nonalcoholic fatty liver disease disrupts triglyceride hydrolysis. J Biol Chem (2009) 3.41
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PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics (2003) 3.23
The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology. Proc Natl Acad Sci U S A (2007) 3.11
Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response. Immunity (2012) 3.07
EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance. Cell (2013) 2.63
Atypical angiopoietin-like protein that regulates ANGPTL3. Proc Natl Acad Sci U S A (2012) 2.62
Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol Cell (2007) 2.56
Secreted kinase phosphorylates extracellular proteins that regulate biomineralization. Science (2012) 2.55
Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer. Am J Hum Genet (2008) 2.53
An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis. Science (2009) 2.49
Evolution of protein structures and functions. Curr Opin Struct Biol (2002) 2.38
Purified NPC1 protein: II. Localization of sterol binding to a 240-amino acid soluble luminal loop. J Biol Chem (2007) 2.34
C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science (2009) 2.04
The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes. Genes Dev (2008) 1.95
Fido, a novel AMPylation domain common to fic, doc, and AvrB. PLoS One (2009) 1.92
CASP9 assessment of free modeling target predictions. Proteins (2011) 1.90
Detecting distant homology with Meta-BASIC. Nucleic Acids Res (2004) 1.86
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res (2006) 1.85
Side-chain modeling with an optimized scoring function. Protein Sci (2002) 1.84
Sequence and structure classification of kinases. J Mol Biol (2002) 1.84
CASP9 target classification. Proteins (2011) 1.75
CASP5 assessment of fold recognition target predictions. Proteins (2003) 1.73
Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch. Structure (2003) 1.69
A minimal domain responsible for Munc13 activity. Nat Struct Mol Biol (2005) 1.68
Genetic variation in ANGPTL4 provides insights into protein processing and function. J Biol Chem (2009) 1.64
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics (2006) 1.60
PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods Mol Biol (2014) 1.59
PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 1.58
NESdb: a database of NES-containing CRM1 cargoes. Mol Biol Cell (2012) 1.57
Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database. J Invest Dermatol (2009) 1.57
Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain. J Biol Chem (2010) 1.51
Reconstruction of ancestral protein sequences and its applications. BMC Evol Biol (2004) 1.48
Structural drift: a possible path to protein fold change. Bioinformatics (2004) 1.46
Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Nucleic Acids Res (2005) 1.44
Protein structure prediction for the male-specific region of the human Y chromosome. Proc Natl Acad Sci U S A (2004) 1.43
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. Bioinformatics (2005) 1.41
A comprehensive update of the sequence and structure classification of kinases. BMC Struct Biol (2005) 1.40
Analysis of CASP8 targets, predictions and assessment methods. Database (Oxford) (2009) 1.38
Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. J Biol Chem (2002) 1.38
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. BMC Struct Biol (2007) 1.33
SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family. Biochemistry (2007) 1.31
Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci (2003) 1.26
Practical lessons from protein structure prediction. Nucleic Acids Res (2005) 1.25
Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade. Protein Sci (2005) 1.25
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. BMC Bioinformatics (2004) 1.25
Unusually rapid evolution of Neuroligin-4 in mice. Proc Natl Acad Sci U S A (2008) 1.25
Remote homology between Munc13 MUN domain and vesicle tethering complexes. J Mol Biol (2009) 1.24
Discrete-continuous duality of protein structure space. Curr Opin Struct Biol (2009) 1.24
Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis. J Biol Chem (2003) 1.24
Protein domain of unknown function DUF1023 is an alpha/beta hydrolase. Proteins (2005) 1.23
PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res (2007) 1.20
Evolution of the regulators of G-protein signaling multigene family in mouse and human. Genomics (2002) 1.18
PROCAIN: protein profile comparison with assisting information. Nucleic Acids Res (2009) 1.17
COMPASS server for remote homology inference. Nucleic Acids Res (2007) 1.16
Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD. Structure (2002) 1.15
Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution. Protein Sci (2006) 1.15
Sequence and structural analyses of nuclear export signals in the NESdb database. Mol Biol Cell (2012) 1.15
Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism. Cell (2013) 1.14
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS. Bioinformatics (2007) 1.14
Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6. Proc Natl Acad Sci U S A (2011) 1.13
CREST--a large and diverse superfamily of putative transmembrane hydrolases. Biol Direct (2011) 1.12
PALSSE: a program to delineate linear secondary structural elements from protein structures. BMC Bioinformatics (2005) 1.12
Succination of Keap1 and activation of Nrf2-dependent antioxidant pathways in FH-deficient papillary renal cell carcinoma type 2. Cancer Cell (2011) 1.12
Structurally analogous proteins do exist! Structure (2004) 1.12
Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease. Protein Sci (2004) 1.10
Paramecium bursaria chlorella virus-1 encodes an unusual arginine decarboxylase that is a close homolog of eukaryotic ornithine decarboxylases. J Biol Chem (2004) 1.10
Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. J Mol Biol (2008) 1.08
Crystal structure of Haemophilus influenzae NadR protein. A bifunctional enzyme endowed with NMN adenyltransferase and ribosylnicotinimide kinase activities. J Biol Chem (2002) 1.07
MESSA: MEta-Server for protein Sequence Analysis. BMC Biol (2012) 1.06
A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics (2007) 1.05
Structural classification of thioredoxin-like fold proteins. Proteins (2005) 1.05
Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes Dev (2013) 1.04
Structural analysis and functional implications of the negative mTORC1 regulator REDD1. Biochemistry (2010) 1.04
Structural classification of small, disulfide-rich protein domains. J Mol Biol (2006) 1.03
Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism. Structure (2008) 1.03
The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif. Biol Direct (2009) 1.02
Effective scoring function for protein sequence design. Proteins (2004) 1.01
CASP5 target classification. Proteins (2003) 1.01
Gaps in structurally similar proteins: towards improvement of multiple sequence alignment. Proteins (2004) 1.00
Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily. Cell Cycle (2006) 0.99
Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A (2003) 0.99
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinformatics (2004) 0.99
Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases. Protein Sci (2003) 0.99
Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1. J Mol Biol (2011) 0.97
Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5. J Mol Biol (2004) 0.96
MALISAM: a database of structurally analogous motifs in proteins. Nucleic Acids Res (2007) 0.96