Published in Curr Opin Struct Biol on June 06, 2008
Basis for substrate recognition and distinction by matrix metalloproteinases. Proc Natl Acad Sci U S A (2014) 0.90
Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet (2008) 15.94
Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell (2006) 11.38
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19
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
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Identification of the acyltransferase that octanoylates ghrelin, an appetite-stimulating peptide hormone. Cell (2008) 5.10
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
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
Evolution of the protein repertoire. Science (2003) 4.24
Structural classification of zinc fingers: survey and summary. Nucleic Acids Res (2003) 3.94
Genome trees and the tree of life. Trends Genet (2002) 3.79
Identification of a candidate therapeutic autophagy-inducing peptide. Nature (2013) 3.76
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
Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods (2013) 3.61
Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science (2008) 3.48
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
PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics (2007) 3.26
PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics (2003) 3.23
DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res (2007) 3.18
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
Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res (2003) 2.87
RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol (2011) 2.77
The importance of sequence diversity in the aggregation and evolution of proteins. Nature (2005) 2.70
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
Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol (2004) 2.58
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
DBD: a transcription factor prediction database. Nucleic Acids Res (2006) 2.46
Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol (2006) 2.44
Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer. Proc Natl Acad Sci U S A (2013) 2.41
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
Assembly reflects evolution of protein complexes. Nature (2008) 2.27
3D complex: a structural classification of protein complexes. PLoS Comput Biol (2006) 2.21
The folding and evolution of multidomain proteins. Nat Rev Mol Cell Biol (2007) 2.16
FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics (2006) 2.13
The relationship between domain duplication and recombination. J Mol Biol (2004) 2.08
C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science (2009) 2.04
The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood (2009) 1.97
The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development (2003) 1.96
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
Evolution of protein complexes by duplication of homomeric interactions. Genome Biol (2007) 1.88
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
Supra-domains: evolutionary units larger than single protein domains. J Mol Biol (2004) 1.82
Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell (2012) 1.80
Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet (2005) 1.75
CASP9 target classification. Proteins (2011) 1.75
CASP5 assessment of fold recognition target predictions. Proteins (2003) 1.73
The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci (2006) 1.71
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
Statistical analysis of domains in interacting protein pairs. Bioinformatics (2004) 1.64
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
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain. J Biol Chem (2010) 1.51
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res (2009) 1.48
Reconstruction of ancestral protein sequences and its applications. BMC Evol Biol (2004) 1.48
Novel specificities emerge by stepwise duplication of functional modules. Genome Res (2005) 1.47
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
Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia. J Exp Med (2013) 1.40
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
Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. Trends Genet (2003) 1.34
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
Functional protein divergence in the evolution of Homo sapiens. Genome Biol (2008) 1.32
SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family. Biochemistry (2007) 1.31
Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genome Res (2003) 1.29
Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res (2008) 1.28
Assessing computational methods of cis-regulatory module prediction. PLoS Comput Biol (2010) 1.27
Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci (2003) 1.26
Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade. Protein Sci (2005) 1.25
Practical lessons from protein structure prediction. Nucleic Acids Res (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
BloodExpress: a database of gene expression in mouse haematopoiesis. Nucleic Acids Res (2008) 1.24