Published in Nat Protoc on January 01, 2007
A specificity map for the PDZ domain family. PLoS Biol (2008) 3.16
PDZ domains and their binding partners: structure, specificity, and modification. Cell Commun Signal (2010) 2.07
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol (2009) 1.78
System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Mol Cell (2016) 1.49
Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proc Natl Acad Sci U S A (2014) 1.34
Conformational stabilization of ubiquitin yields potent and selective inhibitors of USP7. Nat Chem Biol (2012) 1.20
Characterizing WW domain interactions of tumor suppressor WWOX reveals its association with multiprotein networks. J Biol Chem (2014) 1.19
The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol (2011) 1.14
Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods (2012) 1.06
Synthetic human monoclonal antibodies toward staphylococcal enterotoxin B (SEB) protective against toxic shock syndrome. J Biol Chem (2012) 1.04
Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes. Proc Natl Acad Sci U S A (2014) 0.99
Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome. PLoS One (2011) 0.98
SH3 interactome conserves general function over specific form. Mol Syst Biol (2013) 0.94
High-throughput analysis of peptide-binding modules. Proteomics (2012) 0.93
MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics (2010) 0.93
Quantifying protein-protein interactions in high throughput using protein domain microarrays. Nat Protoc (2010) 0.91
Structural snapshots reveal distinct mechanisms of procaspase-3 and -7 activation. Proc Natl Acad Sci U S A (2013) 0.91
Identification of a small peptide that inhibits PCSK9 protein binding to the low density lipoprotein receptor. J Biol Chem (2013) 0.90
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. Nucleic Acids Res (2011) 0.89
Phage display of tissue inhibitor of metalloproteinases-2 (TIMP-2): identification of selective inhibitors of collagenase-1 (metalloproteinase 1 (MMP-1)). J Biol Chem (2011) 0.86
Improvements to the Kunkel mutagenesis protocol for constructing primary and secondary phage-display libraries. Methods (2012) 0.84
A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. Bioinformatics (2013) 0.84
Turning on caspases with genetics and small molecules. Methods Enzymol (2014) 0.83
Isolation of monobodies that bind specifically to the SH3 domain of the Fyn tyrosine protein kinase. N Biotechnol (2011) 0.83
A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening. Genome Med (2014) 0.82
Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps. BMC Biol (2011) 0.82
Anti-idiotypic monobodies for immune response profiling. Methods (2012) 0.79
Protein engineering by highly parallel screening of computationally designed variants. Sci Adv (2016) 0.79
WW domains of the yes-kinase-associated-protein (YAP) transcriptional regulator behave as independent units with different binding preferences for PPxY motif-containing ligands. PLoS One (2015) 0.78
Probing the functions of the paramyxovirus glycoproteins F and HN with a panel of synthetic antibodies. J Virol (2014) 0.78
Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists. Nat Struct Mol Biol (2017) 0.78
Protein and Antibody Engineering by Phage Display. Methods Enzymol (2016) 0.78
Magnetite Biomineralization in Magnetospirillum magneticum Is Regulated by a Switch-like Behavior in the HtrA Protease MamE. J Biol Chem (2016) 0.77
Motif mediated protein-protein interactions as drug targets. Cell Commun Signal (2016) 0.76
Development and characterization of recombinant antibody fragments that recognize and neutralize in vitro Stx2 toxin from Shiga toxin-producing Escherichia coli. PLoS One (2015) 0.76
Discovery and Characterization of a Potent Interleukin-6 Binding Peptide with Neutralizing Activity In Vivo. PLoS One (2015) 0.76
The development and application of a quantitative peptide microarray based approach to protein interaction domain specificity space. Mol Cell Proteomics (2014) 0.76
Anti-idiotypic monobodies derived from a fibronectin scaffold. Biochemistry (2013) 0.75
Multivalent pIX phage display selects for distinct and improved antibody properties. Sci Rep (2016) 0.75
Development and characterization of synthetic antibodies binding to the cystic fibrosis conductance regulator. MAbs (2016) 0.75
Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif. Protein Sci (2017) 0.75
Peptide binding properties of the three PDZ domains of Bazooka (Drosophila Par-3). PLoS One (2014) 0.75
Phage-displayed combinatorial peptide libraries in fusion to beta-lactamase as reporter for an accelerated clone screening: Potential uses of selected enzyme-linked affinity reagents in downstream applications. Comb Chem High Throughput Screen (2010) 0.75
Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. FEBS Lett (2016) 0.75
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. BMC Bioinformatics (2016) 0.75
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
The genetic landscape of a cell. Science (2010) 16.52
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell (2005) 10.41
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature (2007) 9.25
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell (2005) 7.21
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (2001) 7.08
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol (2003) 6.79
An empirical framework for binary interactome mapping. Nat Methods (2008) 6.59
Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell (2006) 6.42
Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol (2003) 5.60
Role of formins in actin assembly: nucleation and barbed-end association. Science (2002) 5.47
Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell (2008) 5.37
Exploration of essential gene functions via titratable promoter alleles. Cell (2004) 5.21
Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell (2005) 4.95
Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol Biol (2006) 4.45
A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. Mol Cell (2003) 4.04
Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell (2006) 4.03
Identification of a bacterial type III effector family with G protein mimicry functions. Cell (2006) 3.47
A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc Natl Acad Sci U S A (2002) 3.46
Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A (2004) 3.18
A specificity map for the PDZ domain family. PLoS Biol (2008) 3.16
The synthetic genetic interaction spectrum of essential genes. Nat Genet (2005) 3.06
eSGA: E. coli synthetic genetic array analysis. Nat Methods (2008) 3.01
Formins direct Arp2/3-independent actin filament assembly to polarize cell growth in yeast. Nat Cell Biol (2002) 2.95
Genotype to phenotype: a complex problem. Science (2010) 2.92
High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol (2007) 2.88
Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol Microbiol (2003) 2.84
Formin leaky cap allows elongation in the presence of tight capping proteins. Curr Biol (2003) 2.69
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol (2005) 2.68
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods (2010) 2.67
The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast. Nat Genet (2007) 2.58
Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell Biol (2003) 2.46
Systematic mapping of genetic interaction networks. Annu Rev Genet (2009) 2.43
Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol (2012) 2.40
Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A (2006) 2.39
Crystal structure of full-length KcsA in its closed conformation. Proc Natl Acad Sci U S A (2009) 2.35
RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex. EMBO J (2005) 2.34
Identification of protein complexes required for efficient sister chromatid cohesion. Mol Biol Cell (2004) 2.34
Formins: signaling effectors for assembly and polarization of actin filaments. J Cell Sci (2003) 2.31
Signature-tagged mutagenesis: barcoding mutants for genome-wide screens. Nat Rev Genet (2006) 2.30
Formins direct Arp2/3-independent actin filament assembly to polarize cell growth in yeast. Nat Cell Biol (2002) 2.27
Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol (2011) 2.26
Regulation of a late phase of T cell polarity and effector functions by Crtam. Cell (2008) 2.18
Mechanism of formin-induced nucleation of actin filaments. Biochemistry (2003) 2.18
Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. Proc Natl Acad Sci U S A (2004) 2.17
Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature (2009) 2.14
High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. J Mol Biol (2004) 2.14
Elg1 forms an alternative RFC complex important for DNA replication and genome integrity. EMBO J (2003) 2.03
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A (2008) 2.01
Golgi targeting of ARF-like GTPase Arl3p requires its Nalpha-acetylation and the integral membrane protein Sys1p. Nat Cell Biol (2004) 1.94
Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation. Science (2012) 1.92
Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation. J Cell Biol (2008) 1.92
Systematic exploration of synergistic drug pairs. Mol Syst Biol (2011) 1.89
Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome. Genes Dev (2011) 1.89
Molecular recognition by a binary code. J Mol Biol (2005) 1.85
Rapid evolution of functional complexity in a domain family. Sci Signal (2009) 1.85
The phosphatidylinositol 4,5-biphosphate and TORC2 binding proteins Slm1 and Slm2 function in sphingolipid regulation. Mol Cell Biol (2006) 1.79
High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants. Genetics (2002) 1.78
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol (2009) 1.78
Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell. Nat Biotechnol (2011) 1.77
Synthetic genetic array analysis of the PtdIns 4-kinase Pik1p identifies components in a Golgi-specific Ypt31/rab-GTPase signaling pathway. Mol Biol Cell (2004) 1.76
A therapeutic antibody targeting BACE1 inhibits amyloid-β production in vivo. Sci Transl Med (2011) 1.75
Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Methods Enzymol (2010) 1.73
Systematic yeast synthetic lethal and synthetic dosage lethal screens identify genes required for chromosome segregation. Proc Natl Acad Sci U S A (2005) 1.72
Global gene deletion analysis exploring yeast filamentous growth. Science (2012) 1.67
The type III effector EspF coordinates membrane trafficking by the spatiotemporal activation of two eukaryotic signaling pathways. J Cell Biol (2007) 1.66
Inhibition of Wnt signaling by Dishevelled PDZ peptides. Nat Chem Biol (2009) 1.65
The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. ACS Chem Biol (2009) 1.65
The interaction network of the chaperonin CCT. EMBO J (2008) 1.63
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
A network of multi-tasking proteins at the DNA replication fork preserves genome stability. PLoS Genet (2005) 1.61
Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J Biol Chem (2006) 1.59
The Erbin PDZ domain binds with high affinity and specificity to the carboxyl termini of delta-catenin and ARVCF. J Biol Chem (2002) 1.59
Genome-wide lethality screen identifies new PI4,5P2 effectors that regulate the actin cytoskeleton. EMBO J (2004) 1.59
Mode of selection and experimental evolution of antifungal drug resistance in Saccharomyces cerevisiae. Genetics (2003) 1.57
Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers. Nat Methods (2008) 1.56
Global map of SUMO function revealed by protein-protein interaction and genetic networks. Mol Cell (2009) 1.55
Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A (2007) 1.51
Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families. J Biol Chem (2006) 1.49
The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae. Genetics (2004) 1.49
Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain. J Biol Chem (2002) 1.49
Mrc1 is required for sister chromatid cohesion to aid in recombination repair of spontaneous damage. Mol Cell Biol (2004) 1.48
Problems with co-funding in Canada. Science (2005) 1.48
An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae. BMC Genet (2005) 1.47
A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. J Mol Biol (2008) 1.45
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res (2008) 1.44
A strategy for modulation of enzymes in the ubiquitin system. Science (2013) 1.43
Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity. J Biol Chem (2006) 1.43
DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res (2009) 1.41
The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. J Mol Biol (2008) 1.41
Two-state selection of conformation-specific antibodies. Proc Natl Acad Sci U S A (2009) 1.40
Synthetic lethal analysis implicates Ste20p, a p21-activated potein kinase, in polarisome activation. Mol Biol Cell (2003) 1.37
Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J Cell Biol (2010) 1.36
Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol Biosyst (2010) 1.35