Published in Nucleic Acids Res on January 01, 2005
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
InterProScan: protein domains identifier. Nucleic Acids Res (2005) 18.82
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res (2006) 10.39
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
InterProScan 5: genome-scale protein function classification. Bioinformatics (2014) 8.52
Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res (2014) 6.82
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res (2014) 6.00
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res (2008) 3.07
Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics (2007) 2.56
Protein function annotation by homology-based inference. Genome Biol (2009) 2.20
PSI-2: structural genomics to cover protein domain family space. Structure (2009) 1.92
Experience using web services for biological sequence analysis. Brief Bioinform (2008) 1.78
Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genomics (2007) 1.77
Unraveling protein networks with power graph analysis. PLoS Comput Biol (2008) 1.77
Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. BMC Genomics (2010) 1.60
YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. J Bacteriol (2006) 1.58
A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells. Mol Microbiol (2006) 1.55
A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol (2006) 1.52
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res (2009) 1.50
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet (2015) 1.49
Minke whale genome and aquatic adaptation in cetaceans. Nat Genet (2013) 1.46
Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics (2014) 1.46
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. J Proteomics (2008) 1.38
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics (2011) 1.36
Phytome: a platform for plant comparative genomics. Nucleic Acids Res (2006) 1.35
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol (2008) 1.35
More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PLoS Comput Biol (2010) 1.26
On the extent and origins of genic novelty in the phylum Nematoda. PLoS Negl Trop Dis (2008) 1.25
Sulfur metabolism in the extreme acidophile acidithiobacillus caldus. Front Microbiol (2011) 1.24
Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiol (2005) 1.23
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. BMC Bioinformatics (2007) 1.21
Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res (2006) 1.21
VMD: a community annotation database for oomycetes and microbial genomes. Nucleic Acids Res (2006) 1.18
Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics (2009) 1.18
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. Nucleic Acids Res (2006) 1.17
The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation. BMC Bioinformatics (2008) 1.17
An examination of dynamics crosstalk between SH2 and SH3 domains by hydrogen/deuterium exchange and mass spectrometry. Protein Sci (2005) 1.17
Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. BMC Genomics (2006) 1.15
Real-time ligand binding pocket database search using local surface descriptors. Proteins (2010) 1.12
InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res (2016) 1.08
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. Nucleic Acids Res (2011) 1.07
Exploiting structural classifications for function prediction: towards a domain grammar for protein function. Curr Opin Struct Biol (2009) 1.02
JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture. BMC Bioinformatics (2005) 0.98
Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, carbon fixation in A. ferrooxidans. BMC Microbiol (2010) 0.98
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. Nucleic Acids Res (2008) 0.97
Computer aided selection of candidate vaccine antigens. Immunome Res (2010) 0.95
Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2016) 0.95
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. Cell Mol Life Sci (2009) 0.95
Genome and proteome annotation: organization, interpretation and integration. J R Soc Interface (2009) 0.95
Analysis of bacteria-challenged wild silkmoth, Antheraea mylitta (lepidoptera) transcriptome reveals potential immune genes. BMC Genomics (2006) 0.94
Genome-scale identification and characterization of moonlighting proteins. Biol Direct (2014) 0.92
Developmental gene discovery in a hemimetabolous insect: de novo assembly and annotation of a transcriptome for the cricket Gryllus bimaculatus. PLoS One (2013) 0.91
From sequence to enzyme mechanism using multi-label machine learning. BMC Bioinformatics (2014) 0.90
Role of Homeodomain leucine zipper (HD-Zip) IV transcription factors in plant development and plant protection from deleterious environmental factors. Int J Mol Sci (2013) 0.90
XatA, an AT-1 autotransporter important for the virulence of Xylella fastidiosa Temecula1. Microbiologyopen (2012) 0.89
Bioinformatics in microbial biotechnology--a mini review. Microb Cell Fact (2005) 0.88
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PLoS One (2013) 0.88
Structure- and sequence-based function prediction for non-homologous proteins. J Struct Funct Genomics (2012) 0.87
Dynamics of domain coverage of the protein sequence universe. BMC Genomics (2012) 0.87
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. Nucleic Acids Res (2013) 0.87
First gene cassettes of integrons as targets in finding adaptive genes in metagenomes. Appl Environ Microbiol (2009) 0.86
Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0. BMC Res Notes (2010) 0.86
Identification and characterization of a bacterial glutamic peptidase. BMC Biochem (2010) 0.86
Text mining in cancer gene and pathway prioritization. Cancer Inform (2014) 0.85
Computational characterization of moonlighting proteins. Biochem Soc Trans (2014) 0.85
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. Nucleic Acids Res (2009) 0.85
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. BMC Bioinformatics (2013) 0.84
Protein domain definition should allow for conditional disorder. Protein Sci (2013) 0.82
In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139. Genomics Inform (2015) 0.82
Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins. BMC Proc (2012) 0.82
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. Database (Oxford) (2012) 0.82
Annotation extension through protein family annotation coherence metrics. Front Genet (2013) 0.81
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. Genome Biol Evol (2014) 0.81
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. BMC Genomics (2007) 0.80
MACHOS: Markov clusters of homologous subsequences. Bioinformatics (2008) 0.80
BLAST-based structural annotation of protein residues using Protein Data Bank. Biol Direct (2016) 0.79
The language of the protein universe. Curr Opin Genet Dev (2015) 0.78
A novel role for protein kinase Kin2 in regulating HAC1 mRNA translocation, splicing, and translation. Mol Cell Biol (2014) 0.78
Troponin T isoform expression is modulated during Atlantic halibut metamorphosis. BMC Dev Biol (2007) 0.78
Fine-tuning of protein domain boundary by minimizing potential coiled coil regions. J Biomol NMR (2006) 0.77
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. BMC Bioinformatics (2013) 0.77
Genome-scale prediction of moonlighting proteins using diverse protein association information. Bioinformatics (2016) 0.77
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. BMC Genomics (2015) 0.76
Constitutive overexpression of the TaNF-YB4 gene in transgenic wheat significantly improves grain yield. J Exp Bot (2015) 0.76
FlhF Is Required for Swarming Motility and Full Pathogenicity of Bacillus cereus. Front Microbiol (2016) 0.76
MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses. Genomics Proteomics Bioinformatics (2012) 0.75
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions. PLoS One (2016) 0.75
Noumeavirus replication relies on a transient remote control of the host nucleus. Nat Commun (2017) 0.75
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. Am J Trop Med Hyg (2016) 0.75
Aberrant coordination geometries discovered in the most abundant metalloproteins. Proteins (2017) 0.75
Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. BMC Plant Biol (2016) 0.75
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. Evol Bioinform Online (2015) 0.75
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. Nucleic Acids Res (2006) 0.75
Rv2031c of Mycobacterium tuberculosis: a master regulator of Rv2028-Rv2031 (HspX) operon. Front Microbiol (2015) 0.75
The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. Gigascience (2015) 0.75
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. Gigascience (2017) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
RASMOL: biomolecular graphics for all. Trends Biochem Sci (1995) 33.76
Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res (1988) 32.89
SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res (2003) 25.86
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37
ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res (2000) 18.27
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21
Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem (2003) 13.44
Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
Modular arrangement of proteins as inferred from analysis of homology. Protein Sci (1994) 9.38
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res (2003) 8.66
ProDom: automated clustering of homologous domains. Brief Bioinform (2002) 7.42
Whole genome protein domain analysis using a new method for domain clustering. Comput Chem (1999) 4.13
Geno3D: automatic comparative molecular modelling of protein. Bioinformatics (2002) 3.19
Towards a reliable objective function for multiple sequence alignments. J Mol Biol (2001) 3.07
The PredictProtein server. Nucleic Acids Res (2003) 2.72
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
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res (2003) 8.66
ProDom: automated clustering of homologous domains. Brief Bioinform (2002) 7.42
Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res (2003) 5.10
MicroRNA-155 promotes autoimmune inflammation by enhancing inflammatory T cell development. Immunity (2010) 4.65
Genetic regulation of biological nitrogen fixation. Nat Rev Microbiol (2004) 3.01
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet (2010) 2.20
Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol Plant Microbe Interact (2004) 2.04
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. Nucleic Acids Res (2002) 1.99
Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A (2009) 1.71
Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res (2008) 1.71
ENDscript: a workflow to display sequence and structure information. Bioinformatics (2002) 1.70
Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis. J Bacteriol (2006) 1.70
BRAF-KIAA1549 fusion predicts better clinical outcome in pediatric low-grade astrocytoma. Clin Cancer Res (2011) 1.49
Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011. DNA Res (2013) 1.48
An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing. Plant J (2014) 1.37
Narcisse: a mirror view of conserved syntenies. Nucleic Acids Res (2007) 1.36
Dosimetric and clinical predictors for radiation-induced esophageal injury. Int J Radiat Oncol Biol Phys (2005) 1.26
Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics (2013) 1.23
Specific genes from the potato brown rot strains of Ralstonia solanacearum and their potential use for strain detection. Phytopathology (2009) 1.22
An environmental perspective on metabolism. J Theor Biol (2007) 1.21
BioMAJ: a flexible framework for databanks synchronization and processing. Bioinformatics (2008) 1.14
RBCs labeled at two biotin densities permit simultaneous and repeated measurements of circulating RBC volume. Transfusion (2004) 1.13
Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay. Appl Environ Microbiol (2010) 1.12
Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads. BMC Genomics (2013) 1.11
The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome. BMC Genomics (2008) 1.07
Prospective assessment of dosimetric/physiologic-based models for predicting radiation pneumonitis. Int J Radiat Oncol Biol Phys (2007) 1.05
Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol (2009) 1.02
On the identifiability of metabolic network models. J Math Biol (2012) 0.93
High-Quality Draft Genome Sequence of the Xanthomonas translucens pv. cerealis Pathotype Strain CFBP 2541. Genome Announc (2015) 0.93
The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes. PLoS Comput Biol (2010) 0.92
RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance. Plant Mol Biol (2015) 0.91
Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101. Protein Sci (2002) 0.89
A gene-phenotype network based on genetic variability for drought responses reveals key physiological processes in controlled and natural environments. PLoS One (2012) 0.88
Development of Sinorhizobium meliloti pilot macroarrays for transcriptome analysis. Appl Environ Microbiol (2003) 0.87
FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti. Microbiology (2004) 0.86
High-quality sequence clustering guided by network topology and multiple alignment likelihood. Bioinformatics (2012) 0.85
Somatostatin receptor imaging of non-small cell lung cancer with 99mTc depreotide. Semin Nucl Med (2002) 0.84
Tissue factor-mediated activation of the prothrombin complex concentrate (PCC) is differently inhibited by dabigatran, rivaroxaban, and apixaban: potential clinical implication. Clin Appl Thromb Hemost (2013) 0.83
Nitrogen regulation in Sinorhizobium meliloti probed with whole genome arrays. FEMS Microbiol Lett (2004) 0.83
Targeted radiopharmaceutical therapy for advanced lung cancer: phase I trial of rhenium Re188 P2045, a somatostatin analog. J Thorac Oncol (2009) 0.82
Preliminary report of the 6-minute walk test as a predictor of radiation-induced pulmonary toxicity. Int J Radiat Oncol Biol Phys (2005) 0.81
Effects of intravenous amino acid administration with Y-90 DOTA-Phe1-Tyr3-Octreotide (SMT487[OctreoTher) treatment. Cancer Biother Radiopharm (2004) 0.80
Two distinct classes of FixJ binding sites defined by in vitro selection. FEBS Lett (2002) 0.80
Radiation-induced narrowing of the tracheobronchial tree: an in-depth analysis. Lung Cancer (2006) 0.79
Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli. J Theor Biol (2011) 0.79
The plant pathogen Xanthomonas campestris pv. campestris exploits N-acetylglucosamine during infection. MBio (2014) 0.78
Identification of metabolic network models from incomplete high-throughput datasets. Bioinformatics (2011) 0.78
Accelerated removal of antibody-coated red blood cells from the circulation is accurately tracked by a biotin label. Transfusion (2011) 0.77
RNA-Seq profile of flavescence dorée phytoplasma in grapevine. BMC Genomics (2014) 0.76
99mTc-depreotide tumour uptake in patients with non-Hodgkin's lymphoma. Nucl Med Commun (2004) 0.75
Compositional differences in commercially available prothrombin complex concentrates. Clin Appl Thromb Hemost (2013) 0.75
Incidental Meningioma Detected on 18F-Fluoride With PET/CT During Initial Staging for Prostate Cancer. Clin Nucl Med (2015) 0.75