Published in Nucleic Acids Res on January 01, 2002
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Rfam: an RNA family database. Nucleic Acids Res (2003) 22.93
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res (2003) 17.39
LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res (2002) 13.61
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res (2006) 10.39
The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res (2004) 8.23
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant Physiol (2003) 3.96
The ERGO genome analysis and discovery system. Nucleic Acids Res (2003) 3.89
The PEDANT genome database. Nucleic Acids Res (2003) 3.47
E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res (2004) 3.43
Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6. J Bacteriol (2006) 3.40
Evolution of sensory complexity recorded in a myxobacterial genome. Proc Natl Acad Sci U S A (2006) 3.35
The European Bioinformatics Institute's data resources. Nucleic Acids Res (2003) 3.34
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res (2003) 3.12
Ubiquitin interactions of NZF zinc fingers. EMBO J (2004) 2.72
The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol (2008) 2.71
MBGD: microbial genome database for comparative analysis. Nucleic Acids Res (2003) 2.60
Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis. PLoS One (2009) 2.38
iProClass: an integrated database of protein family, function and structure information. Nucleic Acids Res (2003) 2.36
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics (2007) 2.31
The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J Bacteriol (2004) 1.97
Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiol (2004) 1.94
Refinement and prediction of protein prenylation motifs. Genome Biol (2005) 1.84
Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. Proc Natl Acad Sci U S A (2007) 1.81
Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc Natl Acad Sci U S A (2002) 1.81
von Hippel-Lindau protein binds hyperphosphorylated large subunit of RNA polymerase II through a proline hydroxylation motif and targets it for ubiquitination. Proc Natl Acad Sci U S A (2003) 1.78
The cholesterol-regulated StarD4 gene encodes a StAR-related lipid transfer protein with two closely related homologues, StarD5 and StarD6. Proc Natl Acad Sci U S A (2002) 1.76
SPD--a web-based secreted protein database. Nucleic Acids Res (2005) 1.75
Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4. J Biol Chem (2003) 1.72
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. Nucleic Acids Res (2007) 1.72
MolliGen, a database dedicated to the comparative genomics of Mollicutes. Nucleic Acids Res (2004) 1.71
A primer on ankyrin repeat function in TRP channels and beyond. Mol Biosyst (2008) 1.70
A streptococcal protease that degrades CXC chemokines and impairs bacterial clearance from infected tissues. EMBO J (2006) 1.69
Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol (2005) 1.69
Computational identification and characterization of novel genes from legumes. Plant Physiol (2004) 1.67
Identification of App1 as a regulator of phagocytosis and virulence of Cryptococcus neoformans. J Clin Invest (2003) 1.66
Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS One (2008) 1.60
Subcellular targeting of nine calcium-dependent protein kinase isoforms from Arabidopsis. Plant Physiol (2003) 1.56
Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. J Bacteriol (2004) 1.56
Predicting N-terminal myristoylation sites in plant proteins. BMC Genomics (2004) 1.53
LEAping to conclusions: a computational reanalysis of late embryogenesis abundant proteins and their possible roles. BMC Bioinformatics (2003) 1.52
A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin. Genome Biol Evol (2011) 1.51
Global transcriptional response to mammalian temperature provides new insight into Francisella tularensis pathogenesis. BMC Microbiol (2008) 1.49
Arabidopsis vegetative storage protein is an anti-insect acid phosphatase. Plant Physiol (2005) 1.47
Chitin synthesis in Saccharomyces cerevisiae in response to supplementation of growth medium with glucosamine and cell wall stress. Eukaryot Cell (2003) 1.46
Legionella pneumophila type II protein secretion promotes virulence in the A/J mouse model of Legionnaires' disease pneumonia. Infect Immun (2004) 1.46
pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. Biol Direct (2007) 1.46
Functional genomics analysis of Singapore grouper iridovirus: complete sequence determination and proteomic analysis. J Virol (2004) 1.44
Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. J Proteome Res (2006) 1.42
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res (2004) 1.41
Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo. Mol Cell Biol (2004) 1.39
PEP: Predictions for Entire Proteomes. Nucleic Acids Res (2003) 1.39
Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res (2008) 1.36
The nicotinic acetylcholine receptor gene family of the honey bee, Apis mellifera. Genome Res (2006) 1.36
Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis. J Bacteriol (2005) 1.35
New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol (2003) 1.33
Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis. BMC Genomics (2009) 1.32
Selenium metabolism in Trypanosoma: characterization of selenoproteomes and identification of a Kinetoplastida-specific selenoprotein. Nucleic Acids Res (2006) 1.32
HotPatch: a statistical approach to finding biologically relevant features on protein surfaces. J Mol Biol (2007) 1.32
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biol (2007) 1.30
SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Res (2004) 1.26
Viral infection and human disease--insights from minimotifs. Front Biosci (2008) 1.26
A virulence factor of myxoma virus colocalizes with NF-kappaB in the nucleus and interferes with inflammation. J Virol (2004) 1.26
Structural genomics: computational methods for structure analysis. Protein Sci (2003) 1.24
Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol (2007) 1.22
Kinetoplastid PPEF phosphatases: dual acylated proteins expressed in the endomembrane system of Leishmania. Mol Biochem Parasitol (2006) 1.21
The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations. Genome Biol (2002) 1.21
The soluble NAD+-Reducing [NiFe]-hydrogenase from Ralstonia eutropha H16 consists of six subunits and can be specifically activated by NADPH. J Bacteriol (2005) 1.20
Analysis of the cytoplasmic domains of Salmonella FlhA and interactions with components of the flagellar export machinery. J Bacteriol (2004) 1.20
Exclusion of a proton ATPase from the apical membrane is associated with cell polarity and tip growth in Nicotiana tabacum pollen tubes. Plant Cell (2008) 1.19
The ULTRACURVATA2 gene of Arabidopsis encodes an FK506-binding protein involved in auxin and brassinosteroid signaling. Plant Physiol (2004) 1.19
Prevalence and sequence diversity of a factor required for actin-based motility in natural populations of Burkholderia species. J Clin Microbiol (2008) 1.18
MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure. Nucleic Acids Res (2003) 1.18
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biol (2007) 1.18
Mouse matriptase-2: identification, characterization and comparative mRNA expression analysis with mouse hepsin in adult and embryonic tissues. Biochem J (2003) 1.18
IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics (2004) 1.17
Phg2, a kinase involved in adhesion and focal site modeling in Dictyostelium. Mol Biol Cell (2004) 1.17
Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L. ssp. indica). Mol Genet Genomics (2007) 1.15
Modulation of KSR activity in Caenorhabditis elegans by Zn ions, PAR-1 kinase and PP2A phosphatase. EMBO J (2003) 1.15
Identification of a virulence-associated determinant, dihydrolipoamide dehydrogenase (lpd), in Mycoplasma gallisepticum through in vivo screening of transposon mutants. Infect Immun (2006) 1.14
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. Nucleic Acids Res (2005) 1.14
The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay. BMC Genomics (2008) 1.14
Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ Microbiol (2009) 1.14
Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Appl Environ Microbiol (2003) 1.13
Complete genome sequence of Mycoplasma bovis type strain PG45 (ATCC 25523). Infect Immun (2010) 1.12
ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res (2004) 1.12
The metD D-methionine transporter locus of Escherichia coli is an ABC transporter gene cluster. J Bacteriol (2002) 1.11
Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics (2005) 1.11
Prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of Pseudomonas fluorescens strain KU-7. Appl Environ Microbiol (2003) 1.11
Avian papillomaviruses: the parrot Psittacus erithacus papillomavirus (PePV) genome has a unique organization of the early protein region and is phylogenetically related to the chaffinch papillomavirus. BMC Microbiol (2002) 1.11
Swiss EMBnet node web server. Nucleic Acids Res (2003) 1.09
Identification and functional analysis of Joka2, a tobacco member of the family of selective autophagy cargo receptors. Autophagy (2011) 1.09
Allelic heterogeneity in the COH1 gene explains clinical variability in Cohen syndrome. Am J Hum Genet (2004) 1.09
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res (2000) 67.44
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis (1997) 57.27
Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci (1994) 31.96
Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A (1987) 29.26
A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem Sci (1994) 28.36
The PROSITE database, its status in 1999. Nucleic Acids Res (1999) 24.88
The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res (2001) 24.45
Improving the sensitivity of the sequence profile method. Protein Sci (1994) 13.54
A flexible motif search technique based on generalized profiles. Comput Chem (1996) 13.22
Hidden Markov models. Curr Opin Struct Biol (1996) 11.56
Profile analysis. Methods Enzymol (1990) 9.40
The EMBL nucleotide sequence database. Nucleic Acids Res (2001) 5.44
PROSITE: recent developments. Nucleic Acids Res (1994) 4.46
Sequence analysis by electronic mail server. Trends Biochem Sci (1993) 2.94
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus. Nature (2005) 17.47
ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res (2003) 17.39
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem (2003) 13.44
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89
Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics (2009) 8.87
PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform (2002) 8.77
The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. Plant Physiol Biochem (2004) 8.59
The PROSITE database. Nucleic Acids Res (2006) 8.11
PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res (2009) 7.47
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
UniProtKB/Swiss-Prot. Methods Mol Biol (2007) 7.05
Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair. Cell (2007) 6.68
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res (2006) 6.13
The 20 years of PROSITE. Nucleic Acids Res (2007) 6.06
ScanProsite: a reference implementation of a PROSITE scanning tool. Appl Bioinformatics (2002) 5.81
Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science (2005) 5.75
RIP1 is an essential mediator of Toll-like receptor 3-induced NF-kappa B activation. Nat Immunol (2004) 5.74
Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature (2002) 5.38
High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform (2002) 4.95
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics (2003) 4.88
Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature (2008) 4.76
IntEnz, the integrated relational enzyme database. Nucleic Acids Res (2004) 4.65
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
New and continuing developments at PROSITE. Nucleic Acids Res (2012) 4.41
Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res (2002) 3.91
A downstream mediator in the growth repression limb of the jasmonate pathway. Plant Cell (2007) 3.85
PICH, a centromere-associated SNF2 family ATPase, is regulated by Plk1 and required for the spindle checkpoint. Cell (2007) 3.80
Selective autophagy: ubiquitin-mediated recognition and beyond. Nat Cell Biol (2010) 3.74
Identification of KIAA1018/FAN1, a DNA repair nuclease recruited to DNA damage by monoubiquitinated FANCD2. Cell (2010) 3.43
ProRule: a new database containing functional and structural information on PROSITE profiles. Bioinformatics (2005) 3.41
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res (2008) 3.29
NBA1, a new player in the Brca1 A complex, is required for DNA damage resistance and checkpoint control. Genes Dev (2009) 3.23
High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol (2002) 3.04
When ubiquitin meets ubiquitin receptors: a signalling connection. Nat Rev Mol Cell Biol (2003) 2.91
OTULIN antagonizes LUBAC signaling by specifically hydrolyzing Met1-linked polyubiquitin. Cell (2013) 2.91
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature (2008) 2.86
The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci U S A (2011) 2.74
The Microbe browser for comparative genomics. Nucleic Acids Res (2009) 2.71
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
Inhibition of homologous recombination by the PCNA-interacting protein PARI. Mol Cell (2011) 2.61
The Sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics (2002) 2.51
EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res (2006) 2.49
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res (2004) 2.47
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45
Ubiquitin-dependent proteolytic control of SUMO conjugates. J Biol Chem (2007) 2.44
KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet (2010) 2.44
Protein sequence databases. Curr Opin Chem Biol (2004) 2.43
MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function. BMC Biochem (2002) 2.43
A positive feedback loop stabilizes the guanine-nucleotide exchange factor Cdc24 at sites of polarization. EMBO J (2002) 2.39
The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res (2002) 2.30
The structure of the CYLD USP domain explains its specificity for Lys63-linked polyubiquitin and reveals a B box module. Mol Cell (2008) 2.27
F-box-directed CRL complex assembly and regulation by the CSN and CAND1. Mol Cell (2009) 2.21
PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J Appl Crystallogr (2009) 2.19
Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. Cancer Res (2003) 2.15
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol (2012) 2.14
Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature (2009) 2.14
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res (2008) 2.14
A human homolog of yeast Est1 associates with telomerase and uncaps chromosome ends when overexpressed. Curr Biol (2003) 2.14
The conserved protein DCN-1/Dcn1p is required for cullin neddylation in C. elegans and S. cerevisiae. Nature (2005) 2.01
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat (2004) 1.97
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97