Published in Nucleic Acids Res on January 01, 2004
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
The UCSC Genome Browser Database: update 2006. Nucleic Acids Res (2006) 11.05
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res (2006) 7.93
The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res (2007) 5.88
ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res (2005) 5.79
The Saccharomyces cerevisiae Lipin homolog is a Mg2+-dependent phosphatidate phosphatase enzyme. J Biol Chem (2006) 4.37
The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res (2006) 4.27
SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res (2010) 3.34
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol (2009) 3.03
Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet (2005) 2.71
Protein family expansions and biological complexity. PLoS Comput Biol (2006) 2.69
DBD: a transcription factor prediction database. Nucleic Acids Res (2006) 2.46
Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res (2006) 2.30
Control of phospholipid synthesis by phosphorylation of the yeast lipin Pah1p/Smp2p Mg2+-dependent phosphatidate phosphatase. J Biol Chem (2006) 1.99
The evolution of two-component systems in bacteria reveals different strategies for niche adaptation. PLoS Comput Biol (2006) 1.98
Evolution of protein complexes by duplication of homomeric interactions. Genome Biol (2007) 1.88
Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol (2005) 1.85
Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res (2007) 1.79
delayed flowering1 Encodes a basic leucine zipper protein that mediates floral inductive signals at the shoot apex in maize. Plant Physiol (2006) 1.77
A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol (2006) 1.76
Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. Proc Natl Acad Sci U S A (2009) 1.73
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. BMC Genomics (2008) 1.64
The limits of protein sequence comparison? Curr Opin Struct Biol (2005) 1.57
Novel specificities emerge by stepwise duplication of functional modules. Genome Res (2005) 1.47
Genomic scale sub-family assignment of protein domains. Nucleic Acids Res (2006) 1.42
Progress towards mapping the universe of protein folds. Genome Biol (2004) 1.41
SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol (2010) 1.40
Regulation of cytotoxin expression by converging eukaryotic-type and two-component signalling mechanisms in Streptococcus agalactiae. Mol Microbiol (2006) 1.39
Assessing strategies for improved superfamily recognition. Protein Sci (2005) 1.21
Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. J Mol Biol (2007) 1.18
The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol (2007) 1.17
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. Nucleic Acids Res (2006) 1.17
New genes from old: redeployment of dUTPase by herpesviruses. J Virol (2005) 1.17
Making connections between novel transcription factors and their DNA motifs. Genome Res (2005) 1.16
Gene fusions and gene duplications: relevance to genomic annotation and functional analysis. BMC Genomics (2005) 1.15
The SUPERFAMILY 1.75 database in 2014: a doubling of data. Nucleic Acids Res (2014) 1.13
Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach. BMC Genomics (2006) 1.11
Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res (2004) 1.09
Global analysis of chaperone effects using a reconstituted cell-free translation system. Proc Natl Acad Sci U S A (2012) 1.05
Functional conservation of erythropoietin signaling in zebrafish. Blood (2007) 1.05
Distribution of RNA binding protein MOEP19 in the oocyte cortex and early embryo indicates pre-patterning related to blastomere polarity and trophectoderm specification. Dev Biol (2007) 1.02
Statistical limits to the identification of ion channel domains by sequence similarity. J Gen Physiol (2006) 1.02
Identification of the rctA gene, which is required for repression of conjugative transfer of rhizobial symbiotic megaplasmids. J Bacteriol (2005) 1.02
Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin. Mol Biol Evol (2010) 1.01
The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum. J Bacteriol (2007) 1.00
Glycolipid acquisition by human glycolipid transfer protein dramatically alters intrinsic tryptophan fluorescence: insights into glycolipid binding affinity. J Biol Chem (2009) 0.96
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. Genome Biol (2008) 0.95
A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics (2013) 0.95
A MADS box protein interacts with a mating-type protein and is required for fruiting body development in the homothallic ascomycete Sordaria macrospora. Eukaryot Cell (2006) 0.94
Multiple domain insertions and losses in the evolution of the Rab prenylation complex. BMC Evol Biol (2007) 0.92
The p21-activated protein kinase inhibitor Skb15 and its budding yeast homologue are 60S ribosome assembly factors. Mol Cell Biol (2007) 0.92
Subcellular localization and tissue specific expression of amidase 1 from Arabidopsis thaliana. Planta (2006) 0.91
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. Plant J (2013) 0.90
The Saccharomyces cerevisiae actin patch protein App1p is a phosphatidate phosphatase enzyme. J Biol Chem (2012) 0.89
The Arabidopsis thaliana AT PRP39-1 gene, encoding a tetratricopeptide repeat protein with similarity to the yeast pre-mRNA processing protein PRP39, affects flowering time. Plant Cell Rep (2007) 0.88
Structure-based function inference using protein family-specific fingerprints. Protein Sci (2006) 0.88
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. BMC Bioinformatics (2008) 0.87
Human glycolipid transfer protein (GLTP) genes: organization, transcriptional status and evolution. BMC Genomics (2008) 0.87
The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci (2006) 0.87
Plant nucleotide cyclases: an increasingly complex and growing family. Plant Signal Behav (2007) 0.86
Comparative evolutionary genomics of the STAT family of transcription factors. JAKSTAT (2012) 0.86
Molecules involved in the modulation of rapid cell death in Xanthomonas. J Bacteriol (2006) 0.86
Cross-talk phosphorylations by protein kinase C and Pho85p-Pho80p protein kinase regulate Pah1p phosphatidate phosphatase abundance in Saccharomyces cerevisiae. J Biol Chem (2014) 0.86
Two exo-beta-D-glucosaminidases/exochitosanases from actinomycetes define a new subfamily within family 2 of glycoside hydrolases. Biochem J (2006) 0.85
Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philos Trans R Soc Lond B Biol Sci (2006) 0.85
GenDiS: Genomic Distribution of protein structural domain Superfamilies. Nucleic Acids Res (2005) 0.85
Toward a three-dimensional view of protein networks between species. Front Microbiol (2012) 0.85
A framework for protein structure classification and identification of novel protein structures. BMC Bioinformatics (2006) 0.85
An assessment of substitution scores for protein profile-profile comparison. Bioinformatics (2011) 0.85
PAH1-encoded phosphatidate phosphatase plays a role in the growth phase- and inositol-mediated regulation of lipid synthesis in Saccharomyces cerevisiae. J Biol Chem (2013) 0.84
Human glycolipid transfer protein gene (GLTP) expression is regulated by Sp1 and Sp3: involvement of the bioactive sphingolipid ceramide. J Biol Chem (2010) 0.83
Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes. Funct Integr Genomics (2009) 0.83
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. BMC Struct Biol (2006) 0.83
Characterization of the yeast actin patch protein App1p phosphatidate phosphatase. J Biol Chem (2013) 0.82
Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins. BMC Biotechnol (2007) 0.82
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. Nucleic Acids Res (2005) 0.82
Yeast Nem1-Spo7 protein phosphatase activity on Pah1 phosphatidate phosphatase is specific for the Pho85-Pho80 protein kinase phosphorylation sites. J Biol Chem (2014) 0.82
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. PLoS One (2010) 0.81
Structural similarity of genetically interacting proteins. BMC Syst Biol (2008) 0.79
The cadherin superfamily in Anopheles gambiae: a comparative study with Drosophila melanogaster. Comp Funct Genomics (2005) 0.79
Structure of phage protein BC1872 from Bacillus cereus, a singleton with new fold. Proteins (2006) 0.79
Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4-55 PHA synthase and an insight into its catalytic mechanism. BMC Struct Biol (2006) 0.78
Crystal structure of YfeU protein from Haemophilus influenzae: a predicted etherase involved in peptidoglycan recycling. J Struct Funct Genomics (2009) 0.78
ProFAT: a web-based tool for the functional annotation of protein sequences. BMC Bioinformatics (2006) 0.78
FISH--family identification of sequence homologues using structure anchored hidden Markov models. Nucleic Acids Res (2006) 0.77
The discovery of the fat-regulating phosphatidic acid phosphatase gene. Front Biol (Beijing) (2011) 0.77
The evolutionary relationship of the domain architectures in the RhoGEF-containing proteins. Genomics Proteomics Bioinformatics (2005) 0.77
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
Phosphorylation of Yeast Pah1 Phosphatidate Phosphatase by Casein Kinase II Regulates Its Function in Lipid Metabolism. J Biol Chem (2016) 0.76
Crystal structure of an acetyltransferase protein from Vibrio cholerae strain N16961. Proteins (2007) 0.76
Expression and mutational analysis of Autographa californica nucleopolyhedrovirus HCF-1: functional requirements for cysteine residues. J Virol (2005) 0.75
Large-scale analysis of macromolecular crowding effects on protein aggregation using a reconstituted cell-free translation system. Front Microbiol (2015) 0.75
Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis. Protein Eng Des Sel (2015) 0.75
Workshop--Predicting the structure of biological molecules. Comp Funct Genomics (2004) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Profile hidden Markov models. Bioinformatics (1998) 56.04
Creating the gene ontology resource: design and implementation. Genome Res (2001) 55.73
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics (2001) 28.35
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
Hidden Markov models for detecting remote protein homologies. Bioinformatics (1998) 21.29
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol (2001) 15.97
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol (1998) 9.09
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol (2002) 6.96
Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci (2000) 6.23
Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol (2002) 4.99
Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol (2001) 4.69
Evolution of the protein repertoire. Science (2003) 4.24
A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res (2002) 3.76
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res (2002) 3.31
Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res (2001) 2.81
The geometry of domain combination in proteins. J Mol Biol (2002) 1.82
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol (2006) 9.95
A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Comparative genomics of trypanosomatid parasitic protozoa. Science (2005) 5.37
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Global signatures of protein and mRNA expression levels. Mol Biosyst (2009) 4.43
The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res (2006) 4.27
Evolution of the protein repertoire. Science (2003) 4.24
A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res (2002) 3.76
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat (2012) 3.60
SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res (2010) 3.34
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res (2002) 3.31
AGEMAP: a gene expression database for aging in mice. PLoS Genet (2007) 3.22
DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res (2007) 3.18
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res (2008) 3.07
Protein family expansions and biological complexity. PLoS Comput Biol (2006) 2.69
Mouse proteome analysis. Genome Res (2003) 2.69
Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol (2004) 2.58
The generation of new protein functions by the combination of domains. Structure (2007) 2.51
Classification of intrinsically disordered regions and proteins. Chem Rev (2014) 2.48
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48
3D complex: a structural classification of protein complexes. PLoS Comput Biol (2006) 2.21
Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res (2003) 2.15
Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics (2013) 2.12
The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development (2003) 1.96
Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol (2006) 1.82
The geometry of domain combination in proteins. J Mol Biol (2002) 1.82
Supra-domains: evolutionary units larger than single protein domains. J Mol Biol (2004) 1.82
Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet (2006) 1.81
A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol (2006) 1.76
D²P²: database of disordered protein predictions. Nucleic Acids Res (2012) 1.75
Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics (2010) 1.71
A phylogenomic profile of globins. BMC Evol Biol (2006) 1.64
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res (2012) 1.63
SCOP2 prototype: a new approach to protein structure mining. Nucleic Acids Res (2013) 1.55
The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics (2008) 1.54
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res (2012) 1.47
TreeVector: scalable, interactive, phylogenetic trees for the web. PLoS One (2010) 1.45
Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. Proc Natl Acad Sci U S A (2003) 1.42
Glucosinolate biosynthesis: demonstration and characterization of the condensing enzyme of the chain elongation cycle in Eruca sativa. Phytochemistry (2004) 1.41
Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinformatics (2009) 1.36
The evolution and structure prediction of coiled coils across all genomes. J Mol Biol (2010) 1.30
Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes. J Biol Chem (2009) 1.29
Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genome Res (2003) 1.29
Genomic and structural aspects of protein evolution. Biochem J (2009) 1.25
Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proc Natl Acad Sci U S A (2005) 1.22
A daily-updated tree of (sequenced) life as a reference for genome research. Sci Rep (2013) 1.22
MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. J Proteome Res (2011) 1.19
The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol (2007) 1.17
Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics. Arthritis Res Ther (2014) 1.15
Divergence of interdomain geometry in two-domain proteins. Structure (2006) 1.14
Sticking together? Falling apart? Exploring the dynamics of the interactome. Trends Biochem Sci (2008) 1.11
Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins. Mol Plant (2008) 1.07
Next-generation analysis of gene expression regulation--comparing the roles of synthesis and degradation. Mol Biosyst (2015) 1.06
Sequence conservation in families whose members have little or no sequence similarity: the four-helical cytokines and cytochromes. J Mol Biol (2002) 1.05
Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution. Bioessays (2011) 1.01
The selection of acceptable protein mutations. Proc Natl Acad Sci U S A (2007) 0.98
The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis. Am J Pathol (2012) 0.98
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Hum Genomics (2014) 0.98
Mining gene functional networks to improve mass-spectrometry-based protein identification. Bioinformatics (2009) 0.96
A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics (2013) 0.95
The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins. Structure (2004) 0.94
Improving protein secondary structure prediction using a simple k-mer model. Bioinformatics (2010) 0.93
Translation regulation gets its 'omics' moment. Wiley Interdiscip Rev RNA (2013) 0.92
Evolution of oligomeric state through geometric coupling of protein interfaces. Proc Natl Acad Sci U S A (2012) 0.92
Evolutionarily consistent families in SCOP: sequence, structure and function. BMC Struct Biol (2012) 0.92
A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation. RNA Biol (2009) 0.91
Ubiquitin--molecular mechanisms for recognition of different structures. Curr Opin Struct Biol (2010) 0.91
VH gene segments in the mouse and human genomes. J Mol Biol (2004) 0.90
Expression and in silico structural analysis of a rice (Oryza sativa) hemoglobin 5. Plant Physiol Biochem (2008) 0.90
Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. BMC Genomics (2008) 0.89
A disease-drug-phenotype matrix inferred by walking on a functional domain network. Mol Biosyst (2013) 0.88
Statistical approach to protein quantification. Mol Cell Proteomics (2013) 0.86
Proteins with class alpha/beta fold have high-level participation in fusion events. J Mol Biol (2002) 0.86
Sequences and topology: intrinsic disorder in the evolving universe of protein structure. Curr Opin Struct Biol (2011) 0.85
Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae. Genome Res (2002) 0.85
Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes. Nucleic Acids Res (2003) 0.84
PECA: a novel statistical tool for deconvoluting time-dependent gene expression regulation. J Proteome Res (2013) 0.83
RNA binding protein-mediated post-transcriptional gene regulation in medulloblastoma. Mol Cells (2014) 0.82
Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. Wiley Interdiscip Rev RNA (2014) 0.81
Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains. J Proteome Res (2014) 0.81
gCMAP: user-friendly connectivity mapping with R. Bioinformatics (2013) 0.81