PIRSF: family classification system at the Protein Information Resource.

The RAST Server: rapid annotations using subsystems technology. BMC Genomics (2008) 175.18

UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05

The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66

The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res (2009) 19.70

InterProScan: protein domains identifier. Nucleic Acids Res (2005) 18.82

InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53

The universal protein resource (UniProt). Nucleic Acids Res (2007) 16.33

The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res (2008) 14.82

The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res (2005) 13.37

New developments in the InterPro database. Nucleic Acids Res (2007) 12.49

The Universal Protein Resource (UniProt). Nucleic Acids Res (2006) 11.50

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res (2006) 10.39

InterProScan 5: genome-scale protein function classification. Bioinformatics (2014) 8.52

Framework for a protein ontology. BMC Bioinformatics (2007) 5.24

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

FIGfams: yet another set of protein families. Nucleic Acids Res (2009) 3.26

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res (2008) 3.07

PIRSF family classification system for protein functional and evolutionary analysis. Evol Bioinform Online (2007) 3.03

clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics (2011) 2.56

DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinformatics (2005) 2.33

Protein function annotation by homology-based inference. Genome Biol (2009) 2.20

HMMER web server: 2015 update. Nucleic Acids Res (2015) 1.98

Comparative genomics of protoploid Saccharomycetaceae. Genome Res (2009) 1.96

The PEDANT genome database in 2005. Nucleic Acids Res (2005) 1.88

The InterPro BioMart: federated query and web service access to the InterPro Resource. Database (Oxford) (2011) 1.75

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics (2014) 1.56

Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. Nucleic Acids Res (2008) 1.56

GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res (2009) 1.50

Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics (2014) 1.46

Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. J Proteome Res (2006) 1.42

Phytome: a platform for plant comparative genomics. Nucleic Acids Res (2006) 1.35

PRIDB: a Protein-RNA interface database. Nucleic Acids Res (2010) 1.33

The Ensembl gene annotation system. Database (Oxford) (2016) 1.31

Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucleic Acids Res (2006) 1.28

Large scale hierarchical clustering of protein sequences. BMC Bioinformatics (2005) 1.28

Quantitative assessment of dictionary-based protein named entity tagging. J Am Med Inform Assoc (2006) 1.19

ProGMap: an integrated annotation resource for protein orthology. Nucleic Acids Res (2009) 1.17

Plant protein annotation in the UniProt Knowledgebase. Plant Physiol (2005) 1.15

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). Database (Oxford) (2014) 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

FastBLAST: homology relationships for millions of proteins. PLoS One (2008) 1.06

Update on genome completion and annotations: Protein Information Resource. Hum Genomics (2004) 1.01

Identification of sensory and signal-transducing domains in two-component signaling systems. Methods Enzymol (2007) 0.96

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. Cell Mol Life Sci (2009) 0.95

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

Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. BMC Genomics (2009) 0.90

The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. Nucleic Acids Res (2005) 0.89

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach. BMC Struct Biol (2013) 0.88

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. Adv Bioinformatics (2010) 0.87

Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PLoS One (2012) 0.87

Significant speedup of database searches with HMMs by search space reduction with PSSM family models. Bioinformatics (2009) 0.86

TGF-beta signaling proteins and the Protein Ontology. BMC Bioinformatics (2009) 0.86

Human neuroglobin protein in cerebrospinal fluid. Proteome Sci (2005) 0.85

A tutorial on protein ontology resources for proteomic studies. Methods Mol Biol (2011) 0.84

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. Database (Oxford) (2012) 0.82

Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. BMC Bioinformatics (2011) 0.82

Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand Genomic Sci (2014) 0.82

In silico characterization of thermostable lipases. Extremophiles (2010) 0.81

Orthology for comparative genomics in the mouse genome database. Mamm Genome (2015) 0.80

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. BMC Bioinformatics (2014) 0.80

Automatically extracting functionally equivalent proteins from SwissProt. BMC Bioinformatics (2008) 0.79

FR database 1.0: a resource focused on fruit development and ripening. Database (Oxford) (2015) 0.79

BLAST-based structural annotation of protein residues using Protein Data Bank. Biol Direct (2016) 0.79

Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function. PLoS Comput Biol (2008) 0.79

Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PLoS One (2016) 0.79

Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PLoS One (2015) 0.78

Quantitative proteomics of Spodoptera frugiperda cells during growth and baculovirus infection. PLoS One (2011) 0.78

Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PLoS One (2012) 0.78

The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. Gigascience (2015) 0.75

GFam: a platform for automatic annotation of gene families. Nucleic Acids Res (2012) 0.75

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res (2017) 0.75

Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins. BMC Bioinformatics (2006) 0.75

Interaction profile-based protein classification of death domain. BMC Bioinformatics (2004) 0.75

Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. PLoS Comput Biol (2016) 0.75

Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. Database (Oxford) (2015) 0.75

Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp. Genome Biol Evol (2016) 0.75

Standards and ontologies for functional genomics 2. Comp Funct Genomics (2004) 0.75

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

The Pfam protein families database. Nucleic Acids Res (2002) 51.34

UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05

The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72

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

Maximum discrimination hidden Markov models of sequence consensus. J Comput Biol (1995) 15.75

The Protein Information Resource. Nucleic Acids Res (2003) 11.17

Superfamily classification in PIR-International Protein Sequence Database. Methods Enzymol (1996) 9.85

The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res (2003) 8.36

The origin and evolution of protein superfamilies. Fed Proc (1976) 6.22

Protein family classification and functional annotation. Comput Biol Chem (2003) 6.06

iProClass: an integrated database of protein family, function and structure information. Nucleic Acids Res (2003) 2.36

The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98

UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05

The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66

The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70

UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics (2007) 17.43

CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res (2003) 14.38

The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res (2002) 12.20

The Protein Information Resource. Nucleic Acids Res (2003) 11.17

PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res (2009) 11.05

Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics (2009) 8.87

MMDB: Entrez's 3D-structure database. Nucleic Acids Res (2003) 6.14

Protein family classification and functional annotation. Comput Biol Chem (2003) 6.06

Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One (2011) 5.64

The pediatric preclinical testing program: description of models and early testing results. Pediatr Blood Cancer (2007) 5.28

Adeno-associated virus serotype 8 efficiently delivers genes to muscle and heart. Nat Biotechnol (2005) 5.27

Framework for a protein ontology. BMC Bioinformatics (2007) 5.24

The iProClass integrated database for protein functional analysis. Comput Biol Chem (2004) 4.97

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94

An overview of the PubChem BioAssay resource. Nucleic Acids Res (2009) 4.75

Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proc Natl Acad Sci U S A (2008) 4.07

Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. Cell (2004) 3.98

PubChem's BioAssay Database. Nucleic Acids Res (2011) 3.74

The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res (2010) 3.74

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72

BioThesaurus: a web-based thesaurus of protein and gene names. Bioinformatics (2005) 3.43

CXCL12 / CXCR4 / CXCR7 chemokine axis and cancer progression. Cancer Metastasis Rev (2010) 3.24

Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A (2007) 3.06

PIRSF family classification system for protein functional and evolutionary analysis. Evol Bioinform Online (2007) 3.03

Protein Information Resource: a community resource for expert annotation of protein data. Nucleic Acids Res (2001) 3.01

Coordination of Rab8 and Rab11 in primary ciliogenesis. Proc Natl Acad Sci U S A (2010) 2.88

S-nitrosohemoglobin deficiency: a mechanism for loss of physiological activity in banked blood. Proc Natl Acad Sci U S A (2007) 2.77

Identification of the enzymatic mechanism of nitroglycerin bioactivation. Proc Natl Acad Sci U S A (2002) 2.65

Amine-controlled assembly of metal-sulfite architecture from 1D chains to 3D framework. Inorg Chem (2007) 2.57

Plasmon-controlled fluorescence: a new paradigm in fluorescence spectroscopy. Analyst (2008) 2.45

Autophagy negatively regulates Wnt signalling by promoting Dishevelled degradation. Nat Cell Biol (2010) 2.37

iProClass: an integrated database of protein family, function and structure information. Nucleic Acids Res (2003) 2.36

Fibrin glue in ophthalmology. Indian J Ophthalmol (2009) 2.35

The yak genome and adaptation to life at high altitude. Nat Genet (2012) 2.34

Characterization of sleep in zebrafish and insomnia in hypocretin receptor mutants. PLoS Biol (2007) 2.34

DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinformatics (2005) 2.33

Retinoic acid promotes limb induction through effects on body axis extension but is unnecessary for limb patterning. Curr Biol (2009) 2.22

Early detection of lung adenocarcinoma in sputum by a panel of microRNA markers. Int J Cancer (2010) 2.20

An essential role for mitochondrial aldehyde dehydrogenase in nitroglycerin bioactivation. Proc Natl Acad Sci U S A (2005) 2.18

Dual-modality monitoring of targeted intraarterial delivery of mesenchymal stem cells after transient ischemia. Stroke (2008) 2.18

Population expansion of the poultry fluff louse, Goniocotes gallinae (De Geer, 1778) (Ischnocera, Phthiraptera). Zoolog Sci (2007) 2.16

PubChem BioAssay: 2014 update. Nucleic Acids Res (2013) 2.14

CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinformatics (2002) 2.13

Keratometric astigmatism after ECCE in eastern Nepal. Continuous versus interrupted sutures. Indian J Ophthalmol (2003) 2.13

Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci (2003) 2.12

14-3-3zeta Cooperates with ErbB2 to promote ductal carcinoma in situ progression to invasive breast cancer by inducing epithelial-mesenchymal transition. Cancer Cell (2009) 2.09

Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase. Methods Mol Biol (2011) 2.08

Photo-activated riboflavin therapy of refractory corneal ulcers. Cornea (2012) 2.06

Exo70 interacts with phospholipids and mediates the targeting of the exocyst to the plasma membrane. EMBO J (2007) 2.03