Published in Methods on August 27, 2011
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
The PSIPRED protein structure prediction server. Bioinformatics (2000) 20.58
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol (1999) 15.63
Principles of protein-protein interactions. Proc Natl Acad Sci U S A (1996) 14.51
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
HMMER web server: interactive sequence similarity searching. Nucleic Acids Res (2011) 13.00
MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90
SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res (1999) 11.33
Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res (2010) 11.32
CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res (2008) 10.73
PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res (2003) 10.01
Twilight zone of protein sequence alignments. Protein Eng (1999) 9.83
SMART 6: recent updates and new developments. Nucleic Acids Res (2008) 9.80
Protein disorder prediction: implications for structural proteomics. Structure (2003) 7.93
Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci (1998) 7.88
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (2004) 6.13
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A (2002) 6.00
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res (2009) 5.90
GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res (2003) 5.90
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res (2007) 5.29
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res (2009) 4.55
The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res (2006) 4.27
RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics (2005) 4.18
TargetDB: a target registration database for structural genomics projects. Bioinformatics (2004) 4.17
Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci (1997) 3.00
Dasty and UniProt DAS: a perfect pair for protein feature visualization. Bioinformatics (2005) 2.74
Toward rational protein crystallization: A Web server for the design of crystallizable protein variants. Protein Sci (2007) 2.57
The comprehensive microbial resource. Nucleic Acids Res (2009) 2.46
Entropy and surface engineering in protein crystallization. Acta Crystallogr D Biol Crystallogr (2005) 2.34
XtalPred: a web server for prediction of protein crystallizability. Bioinformatics (2007) 2.26
Predicting intrinsic disorder in proteins: an overview. Cell Res (2009) 2.24
MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics (2006) 2.23
Consequences of membrane protein overexpression in Escherichia coli. Mol Cell Proteomics (2007) 2.11
Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host. PLoS One (2008) 2.07
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
The Membrane Protein Data Bank. Cell Mol Life Sci (2006) 2.07
PSI-2: structural genomics to cover protein domain family space. Structure (2009) 1.92
PIPs: human protein-protein interaction prediction database. Nucleic Acids Res (2008) 1.91
The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium. J Struct Biol (2010) 1.90
TarO: a target optimisation system for structural biology. Nucleic Acids Res (2008) 1.89
The challenge of protein structure determination--lessons from structural genomics. Protein Sci (2007) 1.82
Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nat Biotechnol (2009) 1.78
EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform (2002) 1.77
Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins (2005) 1.71
The Scottish Structural Proteomics Facility: targets, methods and outputs. J Struct Funct Genomics (2010) 1.66
Metabolic control analysis in drug discovery and disease. Nat Biotechnol (2002) 1.59
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol (2004) 1.57
Towards complete sets of farnesylated and geranylgeranylated proteins. PLoS Comput Biol (2007) 1.57
Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics (2010) 1.55
The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory. Acta Crystallogr D Biol Crystallogr (2011) 1.45
Automated technologies and novel techniques to accelerate protein crystallography for structural genomics. Proteomics (2008) 1.43
Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J Mol Biol (2004) 1.40
BIOZON: a hub of heterogeneous biological data. Nucleic Acids Res (2006) 1.39
MagicMatch--cross-referencing sequence identifiers across databases. Bioinformatics (2005) 1.34
Will my protein crystallize? A sequence-based predictor. Proteins (2006) 1.30
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
Protein solubility: sequence based prediction and experimental verification. Bioinformatics (2006) 1.23
ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res (2009) 1.19
A normalised scale for structural genomics target ranking: the OB-Score. FEBS Lett (2006) 1.15
Structural genomics target selection for the New York consortium on membrane protein structure. J Struct Funct Genomics (2009) 1.14
SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics (2009) 1.14
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics (2008) 1.10
SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr (2006) 1.08
Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure? Curr Protein Pept Sci (2007) 1.08
A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli. Bioinformatics (2005) 1.08
Unmet challenges of structural genomics. Curr Opin Struct Biol (2010) 1.06
Predicting protein crystallization propensity from protein sequence. J Struct Funct Genomics (2010) 1.04
Target selection and deselection at the Berkeley Structural Genomics Center. Proteins (2006) 0.98
Influence of sequence changes and environment on intrinsically disordered proteins. PLoS Comput Biol (2009) 0.97
High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all? Acta Crystallogr D Biol Crystallogr (2005) 0.97
A structural genomics initiative on yeast proteins. J Synchrotron Radiat (2002) 0.97
Unlocking the eukaryotic membrane protein structural proteome. Curr Opin Struct Biol (2010) 0.95
Sequence-based prediction of protein crystallization, purification and production propensity. Bioinformatics (2011) 0.95
Target selection for complex structural genomics. Curr Opin Struct Biol (2006) 0.90
A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics (2004) 0.89
XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. Proteins (2011) 0.85
Sequences and topology: intrinsic disorder in the evolving universe of protein structure. Curr Opin Struct Biol (2011) 0.85
Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits. Proteomics (2008) 0.82
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. Nucleic Acids Res (2008) 0.82
Prediction of protein crystallization outcome using a hybrid method. J Struct Biol (2010) 0.82
Structural genomics approach to drug discovery for Mycobacterium tuberculosis. Curr Opin Microbiol (2009) 0.81
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84
The Jalview Java alignment editor. Bioinformatics (2004) 21.74
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res (2006) 4.64
Emerging roles of pseudokinases. Trends Cell Biol (2006) 4.48
OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics (2003) 4.01
Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA (2009) 3.87
System-wide changes to SUMO modifications in response to heat shock. Sci Signal (2009) 3.50
A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science (2011) 2.50
MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics (2006) 2.23
Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput Biol (2009) 2.06
Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins. Biochem J (2010) 1.94
PIPs: human protein-protein interaction prediction database. Nucleic Acids Res (2008) 1.91
TarO: a target optimisation system for structural biology. Nucleic Acids Res (2008) 1.89
The Scottish Structural Proteomics Facility: targets, methods and outputs. J Struct Funct Genomics (2010) 1.66
Classification and functional annotation of eukaryotic protein kinases. Proteins (2007) 1.62
Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res (2010) 1.40
The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol (2007) 1.38
Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res (2011) 1.35
Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods (2010) 1.34
Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation. Nat Struct Mol Biol (2012) 1.34
Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases. EMBO J (2009) 1.32
Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics (2007) 1.31
Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects. J Allergy Clin Immunol (2013) 1.30
Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci U S A (2012) 1.29
PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity. Sci Signal (2012) 1.15
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res (2007) 1.15
A normalised scale for structural genomics target ranking: the OB-Score. FEBS Lett (2006) 1.15
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res (2008) 1.12
The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4. EMBO J (2011) 1.11
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics (2008) 1.10
Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma. Nat Genet (2012) 1.08
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. BMC Bioinformatics (2011) 1.06
The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe. BMC Genomics (2007) 1.04
Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res (2011) 1.04
Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA. Bioinformatics (2011) 1.00
A new family of transcription factors. Development (2008) 0.98
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics (2008) 0.97
Identification of a glycosylphosphatidylinositol anchor-modifying beta1-3 N-acetylglucosaminyl transferase in Trypanosoma brucei. Mol Microbiol (2008) 0.96
The kinomes of apicomplexan parasites. Microbes Infect (2012) 0.96
Quantification of the variation in percentage identity for protein sequence alignments. BMC Bioinformatics (2006) 0.94
Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Mol Biol Cell (2010) 0.94
PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities. BMC Res Notes (2011) 0.92
Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA. PLoS Genet (2013) 0.91
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. BMC Syst Biol (2011) 0.89
Biological units and their effect upon the properties and prediction of protein-protein interactions. J Mol Biol (2006) 0.89
Genome analysis of the unicellular green alga Chlamydomonas reinhardtii Indicates an ancient evolutionary origin for key pattern recognition and cell-signaling protein families. Genetics (2008) 0.88
Increased coverage obtained by combination of methods for protein sequence database searching. Bioinformatics (2003) 0.88
A comparison of SCOP and CATH with respect to domain-domain interactions. Proteins (2008) 0.85
XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. Proteins (2011) 0.85
The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation. Sci Rep (2013) 0.83
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. Nucleic Acids Res (2008) 0.82
Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.81
Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5'-phosphate-dependent aminotransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.81
Elevated O-GlcNAc levels activate epigenetically repressed genes and delay mouse ESC differentiation without affecting naïve to primed cell transition. Stem Cells (2014) 0.80
Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA (2016) 0.76
PNAC: a protein nucleolar association classifier. BMC Genomics (2011) 0.76
Visual representation of database search results: the RHIMS Plot. Bioinformatics (2003) 0.75