Published in PLoS Comput Biol on April 04, 2008
Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature (2009) 2.88
Accurate prediction of peptide binding sites on protein surfaces. PLoS Comput Biol (2009) 1.48
Predictive Bcl-2 family binding models rooted in experiment or structure. J Mol Biol (2012) 1.09
Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction. PLoS Comput Biol (2010) 1.03
Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PLoS Comput Biol (2014) 1.00
A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. Bioinformatics (2010) 0.94
Predicting PDZ domain mediated protein interactions from structure. BMC Bioinformatics (2013) 0.94
Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Res (2009) 0.92
Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data. PLoS One (2013) 0.89
Positively selected sites in cetacean myoglobins contribute to protein stability. PLoS Comput Biol (2013) 0.89
AB-Bind: Antibody binding mutational database for computational affinity predictions. Protein Sci (2015) 0.84
PDZ domain-containing 1 (PDZK1) protein regulates phospholipase C-β3 (PLC-β3)-specific activation of somatostatin by forming a ternary complex with PLC-β3 and somatostatin receptors. J Biol Chem (2012) 0.81
Predicting peptide-mediated interactions on a genome-wide scale. PLoS Comput Biol (2015) 0.79
Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease. Int J Mol Sci (2015) 0.79
Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. Mol Syst Biol (2015) 0.78
Enhanced prediction of Src homology 2 (SH2) domain binding potentials using a fluorescence polarization-derived c-Met, c-Kit, ErbB, and androgen receptor interactome. Mol Cell Proteomics (2014) 0.77
Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design. Methods Mol Biol (2017) 0.75
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
SH2 domains recognize specific phosphopeptide sequences. Cell (1993) 17.28
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res (2003) 15.74
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res (2005) 9.90
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res (2004) 8.23
The BRCT domain is a phospho-protein binding domain. Science (2003) 7.42
Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature (2001) 7.31
The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain. Cell (2003) 7.04
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol (1994) 6.41
The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30
A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature (2005) 5.75
Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell (2004) 5.02
Reading protein modifications with interaction domains. Nat Rev Mol Cell Biol (2006) 4.55
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics (2004) 4.44
Structural basis for phosphoserine-proline recognition by group IV WW domains. Nat Struct Biol (2000) 4.25
Structural analysis of 14-3-3 phosphopeptide complexes identifies a dual role for the nuclear export signal of 14-3-3 in ligand binding. Mol Cell (1999) 4.02
Probabilistic model of the human protein-protein interaction network. Nat Biotechnol (2005) 3.99
Diverse biochemical properties of Shp2 mutants. Implications for disease phenotypes. J Biol Chem (2005) 2.60
Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2. Science (2007) 2.51
Molecular basis for the dephosphorylation of the activation segment of the insulin receptor by protein tyrosine phosphatase 1B. Mol Cell (2000) 2.32
Recognition and specificity in protein tyrosine kinase-mediated signalling. Trends Biochem Sci (1995) 2.31
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A (2005) 2.31
Sustained activation of N-WASP through phosphorylation is essential for neurite extension. Dev Cell (2002) 1.58
Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition. Mol Cell (1999) 1.47
Structural basis for histone and phosphohistone binding by the GCN5 histone acetyltransferase. Mol Cell (2003) 1.47
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor. Proc Natl Acad Sci U S A (2006) 1.45
SH2 domain specificity and activity modified by a single residue. Nature (1994) 1.44
Molecular recognition by SH2 domains. Adv Protein Chem (2002) 1.40
Sequence specificity in recognition of the epidermal growth factor receptor by protein tyrosine phosphatase 1B. J Biol Chem (1993) 1.36
Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. J Mol Biol (2005) 1.33
Investigation of phosphotyrosine recognition by the SH2 domain of the Src kinase. J Mol Biol (1999) 1.24
Biochemical and structural characterization of the interaction of memapsin 2 (beta-secretase) cytosolic domain with the VHS domain of GGA proteins. Biochemistry (2003) 1.23
Calorimetric investigation of proton linkage by monitoring both the enthalpy and association constant of binding: application to the interaction of the Src SH2 domain with a high-affinity tyrosyl phosphopeptide. Biochemistry (1998) 1.21
Kinetics of p56lck and p60src Src homology 2 domain binding to tyrosine-phosphorylated peptides determined by a competition assay or surface plasmon resonance. Proc Natl Acad Sci U S A (1993) 1.18
Phosphoregulation of sorting signal-VHS domain interactions by a direct electrostatic mechanism. Nat Struct Biol (2002) 1.16
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PLoS Comput Biol (2005) 1.15
A "three-pronged" binding mechanism for the SAP/SH2D1A SH2 domain: structural basis and relevance to the XLP syndrome. EMBO J (2002) 1.15
Standard atomic volumes in double-stranded DNA and packing in protein--DNA interfaces. Nucleic Acids Res (2001) 1.14
Thermodynamic studies of tyrosyl-phosphopeptide binding to the SH2 domain of p56lck. Biochemistry (1994) 1.13
Activation of hematopoietic progenitor kinase 1 involves relocation, autophosphorylation, and transphosphorylation by protein kinase D1. Mol Cell Biol (2005) 1.13
Selectivity and promiscuity in the interaction network mediated by protein recognition modules. FEBS Lett (2004) 1.12
Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells. EMBO J (2001) 1.10
Specificity in recognition of phosphopeptides by src-homology 2 domains. J Cell Sci Suppl (1994) 1.07
Characterization of phosphopeptide motifs specific for the Src homology 2 domains of signal transducer and activator of transcription 1 (STAT1) and STAT3. J Biol Chem (2003) 1.04
Structural basis for differential recognition of tyrosine-phosphorylated sites in the linker for activation of T cells (LAT) by the adaptor Gads. EMBO J (2004) 1.00
A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. Protein Sci (2004) 1.00
Stability and peptide binding specificity of Btk SH2 domain: molecular basis for X-linked agammaglobulinemia. Protein Sci (2000) 1.00
The X-linked lymphoproliferative disease gene product SAP associates with PAK-interacting exchange factor and participates in T cell activation. Proc Natl Acad Sci U S A (2006) 1.00
90-kDa ribosomal S6 kinase is a direct target for the nuclear fibroblast growth factor receptor 1 (FGFR1): role in FGFR1 signaling. J Biol Chem (2004) 0.99
Identification of phosphopeptide ligands for the Src-homology 2 (SH2) domain of Grb2 by phage display. Eur J Biochem (1997) 0.98
How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Fold Des (1998) 0.95
A genome-wide Ras-effector interaction network. J Mol Biol (2007) 0.94
Phosphorus-31 nuclear magnetic resonance of phosphoproteins. Methods Enzymol (1989) 0.92
Structural basis for specificity switching of the Src SH2 domain. Mol Cell (2000) 0.91
Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides. Biochemistry (2003) 0.90
An investigation of phosphopeptide binding to SH2 domain. Biochem Biophys Res Commun (2003) 0.89
Structural basis for the specific recognition of RET by the Dok1 phosphotyrosine binding domain. J Biol Chem (2003) 0.89
Prediction of binding sites of peptide recognition domains: an application on Grb2 and SAP SH2 domains. J Mol Biol (2006) 0.87
Comparison of binding energies of SrcSH2-phosphotyrosyl peptides with structure-based prediction using surface area based empirical parameterization. Protein Sci (2000) 0.84
The carboxyl terminus of v-Abl protein can augment SH2 domain function. J Virol (2000) 0.84
The molecular basis of Src kinase specificity during vertebrate mesoderm formation. J Biol Chem (2002) 0.84
Structural and thermodynamic basis for the interaction of the Src SH2 domain with the activated form of the PDGF beta-receptor. J Mol Biol (2003) 0.82
Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains. Proteins (2001) 0.80
pp60v-src transformation of rat cells but not chicken cells strongly correlates with low-affinity phosphopeptide binding by the SH2 domain. Mol Biol Cell (1997) 0.79
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol (2007) 8.88
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol (2004) 7.02
The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Correlation of mRNA and protein in complex biological samples. FEBS Lett (2009) 4.38
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Phenotypic landscape of a bacterial cell. Cell (2010) 3.50
Impact of genome reduction on bacterial metabolism and its regulation. Science (2009) 3.45
Evolvability and hierarchy in rewired bacterial gene networks. Nature (2008) 3.43
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res (2006) 3.04
Gain of function of mutant p53 by coaggregation with multiple tumor suppressors. Nat Chem Biol (2011) 2.94
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92
Structure-based assembly of protein complexes in yeast. Science (2004) 2.89
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods (2010) 2.74
From in vivo to in silico biology and back. Nature (2006) 2.74
The mechanism of γ-Secretase dysfunction in familial Alzheimer disease. EMBO J (2012) 2.72
Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci U S A (2003) 2.71
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res (2005) 2.69
Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol (2006) 2.69
De novo designed peptide-based amyloid fibrils. Proc Natl Acad Sci U S A (2002) 2.59
Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2. Science (2007) 2.51
How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41
Lipids revert inert Abeta amyloid fibrils to neurotoxic protofibrils that affect learning in mice. EMBO J (2007) 2.39
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature (2008) 2.37
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A (2005) 2.31
Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31
Neurotoxicity of Alzheimer's disease Aβ peptides is induced by small changes in the Aβ42 to Aβ40 ratio. EMBO J (2010) 2.26
The stability effects of protein mutations appear to be universally distributed. J Mol Biol (2007) 2.25
Protein aggregation and amyloidosis: confusion of the kinds? Curr Opin Struct Biol (2006) 2.10
A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. J Mol Biol (2004) 2.05
Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol (2005) 2.04
Analysis and description of HOLTIN service provision for AECG monitoring in complex indoor environments. Sensors (Basel) (2013) 2.02
Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs. Mol Cell Proteomics (2008) 2.01
Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci (2005) 1.91
How evolutionary pressure against protein aggregation shaped chaperone specificity. J Mol Biol (2005) 1.91
Computer-aided design of a PDZ domain to recognize new target sequences. Nat Struct Biol (2002) 1.89
Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell (2012) 1.88
Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc Natl Acad Sci U S A (2004) 1.83
Recognizing and defining true Ras binding domains I: biochemical analysis. J Mol Biol (2005) 1.76
Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences. Nucleic Acids Res (2008) 1.74
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics (2006) 1.69
Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res (2009) 1.68
Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol (2006) 1.64
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat Methods (2013) 1.60
Strand-specific deep sequencing of the transcriptome. Genome Res (2010) 1.58
A graphical interface for the FoldX forcefield. Bioinformatics (2011) 1.50
A generative, probabilistic model of local protein structure. Proc Natl Acad Sci U S A (2008) 1.50
Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol (2005) 1.48
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor. Proc Natl Acad Sci U S A (2006) 1.45
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res (2011) 1.44
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res (2007) 1.43
A detailed thermodynamic analysis of ras/effector complex interfaces. J Mol Biol (2004) 1.42
The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci U S A (2005) 1.41
Energy estimation in protein design. Curr Opin Struct Biol (2002) 1.39
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
Redox proteomics of protein-bound methionine oxidation. Mol Cell Proteomics (2011) 1.37
PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res (2009) 1.35
Towards cellular systems in 4D. Cell (2005) 1.33
Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. J Mol Biol (2005) 1.33