CASP5 target classification.

CASP9 assessment of free modeling target predictions. Proteins (2011) 1.90

MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics (2008) 1.88

Target domain definition and classification in CASP8. Proteins (2009) 1.48

Structure-based function inference using protein family-specific fingerprints. Protein Sci (2006) 0.88

An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinformatics (2006) 0.82

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications. J Comput Aided Mol Des (2009) 0.77

Addressing the Role of Conformational Diversity in Protein Structure Prediction. PLoS One (2016) 0.76

A fold-recognition approach to loop modeling. J Mol Model (2005) 0.75

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

SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88

Protein structure comparison by alignment of distance matrices. J Mol Biol (1993) 34.74

RASMOL: biomolecular graphics for all. Trends Biochem Sci (1995) 33.76

An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model (1997) 11.53

DaliLite workbench for protein structure comparison. Bioinformatics (2000) 10.53

Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. Cell (1997) 6.12

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res (2000) 3.56

Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci U S A (2002) 2.92

Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res (1998) 2.61

Atomic structure of the RuvC resolvase: a holliday junction-specific endonuclease from E. coli. Cell (1994) 2.55

Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase. Proc Natl Acad Sci U S A (1993) 2.34

The structure of Escherichia coli cytosine deaminase. J Mol Biol (2002) 1.81

CASP5 assessment of fold recognition target predictions. Proteins (2003) 1.73

Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system. J Biol Chem (1997) 1.71

Crystal structure of the histone acetyltransferase Hpa2: A tetrameric member of the Gcn5-related N-acetyltransferase superfamily. J Mol Biol (1999) 1.70

Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima. Structure (2002) 1.68

The structural basis of ordered substrate binding by serotonin N-acetyltransferase: enzyme complex at 1.8 A resolution with a bisubstrate analog. Cell (1999) 1.62

The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase. Proc Natl Acad Sci U S A (1994) 1.58

Crystal structure of the alpha appendage of AP-2 reveals a recruitment platform for clathrin-coat assembly. Proc Natl Acad Sci U S A (1999) 1.52

Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites. Proc Natl Acad Sci U S A (1996) 1.48

The structure of a binary complex between a mammalian mevalonate kinase and ATP: insights into the reaction mechanism and human inherited disease. J Biol Chem (2002) 1.37

The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase. Nat Struct Biol (1998) 1.35

Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum. J Mol Biol (1998) 1.33

EstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity. Protein Sci (2002) 1.31

Structure of the histidine-containing phosphocarrier protein HPr from Bacillus subtilis at 2.0-A resolution. Proc Natl Acad Sci U S A (1992) 1.26

The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution. J Mol Biol (1995) 1.16

Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases. Nat Struct Biol (2000) 0.96

Structural insights into the ligand binding domains of membrane bound guanylyl cyclases and natriuretic peptide receptors. J Mol Biol (2001) 0.95

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72

SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11

SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21

Ensembl 2011. Nucleic Acids Res (2010) 14.68

Ensembl 2012. Nucleic Acids Res (2011) 14.55

Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44

Ensembl 2014. Nucleic Acids Res (2013) 12.62

Ensembl 2013. Nucleic Acids Res (2012) 11.70

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

Ensembl's 10th year. Nucleic Acids Res (2009) 10.82

The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52

Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res (2002) 7.89

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

Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56

Integrating sequence and structural biology with DAS. BMC Bioinformatics (2007) 5.12

Identification of the acyltransferase that octanoylates ghrelin, an appetite-stimulating peptide hormone. Cell (2008) 5.10

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res (2008) 4.84

MaxBench: evaluation of sequence and structure comparison methods. Bioinformatics (2002) 4.83

Adding some SPICE to DAS. Bioinformatics (2005) 4.62

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

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

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

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

Estrogen receptor (ER) mRNA and ER-related gene expression in breast cancers that are 1% to 10% ER-positive by immunohistochemistry. J Clin Oncol (2012) 2.98

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

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res (2005) 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

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

The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33

SISYPHUS--structural alignments for proteins with non-trivial relationships. Nucleic Acids Res (2006) 2.18

Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. J Natl Cancer Inst (2010) 2.16

Cortical surface shape analysis based on spherical wavelets. IEEE Trans Med Imaging (2007) 2.11

Dalliance: interactive genome viewing on the web. Bioinformatics (2011) 2.07

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

Evaluation of a 30-gene paclitaxel, fluorouracil, doxorubicin, and cyclophosphamide chemotherapy response predictor in a multicenter randomized trial in breast cancer. Clin Cancer Res (2010) 1.81

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

Molecular anatomy of breast cancer stroma and its prognostic value in estrogen receptor-positive and -negative cancers. J Clin Oncol (2010) 1.63

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

Multifactorial approach to predicting resistance to anthracyclines. J Clin Oncol (2011) 1.52

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

Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput Biol (2006) 1.46

Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Nucleic Acids Res (2005) 1.44

Prospective comparison of clinical and genomic multivariate predictors of response to neoadjuvant chemotherapy in breast cancer. Clin Cancer Res (2010) 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

Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res (2008) 1.28

Mutation profiling identifies numerous rare drug targets and distinct mutation patterns in different clinical subtypes of breast cancers. Breast Cancer Res Treat (2012) 1.26

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

Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis. J Biol Chem (2003) 1.24

Discrete-continuous duality of protein structure space. Curr Opin Struct Biol (2009) 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

Different gene expressions are associated with the different molecular subtypes of inflammatory breast cancer. Breast Cancer Res Treat (2010) 1.19

Evolution of the regulators of G-protein signaling multigene family in mouse and human. Genomics (2002) 1.18