Published in Nature on September 22, 2005
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
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A specificity map for the PDZ domain family. PLoS Biol (2008) 3.16
Three-dimensional structures of membrane proteins from genomic sequencing. Cell (2012) 3.02
Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol (2007) 2.28
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Two-component protein-engineered physical hydrogels for cell encapsulation. Proc Natl Acad Sci U S A (2009) 1.63
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An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol (2010) 1.42
Extracting function from a beta-trefoil folding motif. Proc Natl Acad Sci U S A (2008) 1.34
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Novel protein folds and their nonsequential structural analogs. Protein Sci (2008) 1.19
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC Bioinformatics (2006) 1.19
Structures of YAP protein domains reveal promising targets for development of new cancer drugs. Semin Cell Dev Biol (2012) 1.19
Navigating cancer network attractors for tumor-specific therapy. Nat Biotechnol (2012) 1.18
Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity. Proc Natl Acad Sci U S A (2008) 1.11
Ultra-fast evaluation of protein energies directly from sequence. PLoS Comput Biol (2006) 1.11
From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol (2013) 1.03
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Stabilizing proteins from sequence statistics: the interplay of conservation and correlation in triosephosphate isomerase stability. J Mol Biol (2012) 1.03
Structural basis for polyproline recognition by the FE65 WW domain. J Mol Biol (2007) 1.01
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Protein-engineered injectable hydrogel to improve retention of transplanted adipose-derived stem cells. Adv Healthc Mater (2012) 0.94
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Molecular-level engineering of protein physical hydrogels for predictive sol-gel phase behavior. Biomacromolecules (2011) 0.90
How directional translocation is regulated in a DNA helicase motor. Biophys J (2007) 0.89
Epistasis in protein evolution. Protein Sci (2016) 0.88
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Recent progress in protein drug design and discovery with a focus on novel approaches to the development of anti-cocaine medications. Future Med Chem (2009) 0.87
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Integration of evolutionary features for the identification of functionally important residues in major facilitator superfamily transporters. PLoS Comput Biol (2009) 0.86
Hippo signaling is required for Notch-dependent smooth muscle differentiation of neural crest. Development (2015) 0.86
Exploring allosteric coupling in the alpha-subunit of heterotrimeric G proteins using evolutionary and ensemble-based approaches. BMC Struct Biol (2008) 0.86
Optimization of combinatorial mutagenesis. J Comput Biol (2011) 0.85
Adaptable hydrogel networks with reversible linkages for tissue engineering. Adv Mater (2015) 0.85
Protein sectors: statistical coupling analysis versus conservation. PLoS Comput Biol (2015) 0.84
Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. PLoS Comput Biol (2015) 0.84
Interrogating and predicting tolerated sequence diversity in protein folds: application to E. elaterium trypsin inhibitor-II cystine-knot miniprotein. PLoS Comput Biol (2009) 0.83
Circular permutation of a WW domain: folding still occurs after excising the turn of the folding-nucleating hairpin. J Am Chem Soc (2014) 0.81
Allosteric switching of agonist/antagonist activity by a single point mutation in the interluekin-1 receptor antagonist, IL-1Ra. J Mol Biol (2013) 0.81
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models. PLoS Comput Biol (2016) 0.81
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Avidity-controlled hydrogels for injectable co-delivery of induced pluripotent stem cell-derived endothelial cells and growth factors. J Control Release (2014) 0.81
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The Context-Dependence of Mutations: A Linkage of Formalisms. PLoS Comput Biol (2016) 0.80
Designing ECM-mimetic materials using protein engineering. Acta Biomater (2013) 0.80
Accurate simulation and detection of coevolution signals in multiple sequence alignments. PLoS One (2012) 0.79
Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach. PLoS One (2012) 0.79
Versatile communication strategies among tandem WW domain repeats. Exp Biol Med (Maywood) (2015) 0.78
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Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A. J Mol Biol (2008) 0.77
The Expanding Toolbox of In Vivo Bioluminescent Imaging. Front Oncol (2016) 0.77
TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis. BMC Bioinformatics (2009) 0.76
Functional characterisation of the WW minimal domain for delivering therapeutic proteins by adenovirus dodecahedron. PLoS One (2012) 0.76
Towards the computational design of protein post-translational regulation. Bioorg Med Chem (2015) 0.76
Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions. J Comput Aided Mol Des (2013) 0.76
Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software. Sci Rep (2015) 0.75
Selection platforms for directed evolution in synthetic biology. Biochem Soc Trans (2016) 0.75
Crystallization and preliminary X-ray crystallographic analysis of an artificial molten-globular-like triosephosphate isomerase protein of mixed phylogenetic origin. Acta Crystallogr F Struct Biol Commun (2014) 0.75
Allostery Wiring Map for Kinesin Energy Transduction and Its Evolution. J Biol Chem (2016) 0.75
Structural Determinants of Sleeping Beauty Transposase Activity. Mol Ther (2016) 0.75
Structural biology: form and function instructions. Nature (2005) 0.75
Improving the catalytic activity of isopentenyl phosphate kinase through protein coevolution analysis. Sci Rep (2016) 0.75
Production in Pichia pastoris of complementary protein-based polymers with heterodimer-forming WW and PPxY domains. Microb Cell Fact (2016) 0.75
WW domain-binding protein 2: an adaptor protein closely linked to the development of breast cancer. Mol Cancer (2017) 0.75
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res (2003) 15.74
RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly. Cell (2007) 8.71
MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. Cell (2005) 8.39
The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain. Cell (2003) 7.04
Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates. Science (2003) 6.97
Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94
BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science (2003) 6.88
The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science (2011) 6.75
Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol (2003) 6.50
Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell (2012) 5.92
TAZ, a transcriptional modulator of mesenchymal stem cell differentiation. Science (2005) 5.56
A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science (2005) 4.75
Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery. Nature (2008) 4.33
p53-deficient cells rely on ATM- and ATR-mediated checkpoint signaling through the p38MAPK/MK2 pathway for survival after DNA damage. Cancer Cell (2007) 4.01
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
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MAPKAP kinase-2 is a cell cycle checkpoint kinase that regulates the G2/M transition and S phase progression in response to UV irradiation. Mol Cell (2005) 3.48
TAZ controls Smad nucleocytoplasmic shuttling and regulates human embryonic stem-cell self-renewal. Nat Cell Biol (2008) 3.44
Structural determinants of allosteric ligand activation in RXR heterodimers. Cell (2004) 3.36
Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer. Nat Struct Mol Biol (2004) 3.26
Evolutionary information for specifying a protein fold. Nature (2005) 3.23
Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol (2006) 3.18
Kinases that control the cell cycle in response to DNA damage: Chk1, Chk2, and MK2. Curr Opin Cell Biol (2009) 3.15
Hem-1 complexes are essential for Rac activation, actin polymerization, and myosin regulation during neutrophil chemotaxis. PLoS Biol (2006) 3.01
Chemical genetic screen for AMPKα2 substrates uncovers a network of proteins involved in mitosis. Mol Cell (2011) 2.99
14-3-3sigma controls mitotic translation to facilitate cytokinesis. Nature (2007) 2.98
14-3-3 transits to the nucleus and participates in dynamic nucleocytoplasmic transport. J Cell Biol (2002) 2.97
Lamellipodin, an Ena/VASP ligand, is implicated in the regulation of lamellipodial dynamics. Dev Cell (2004) 2.96
Surface sites for engineering allosteric control in proteins. Science (2008) 2.82
Structure and function of Polo-like kinases. Oncogene (2005) 2.72
mTORC1 phosphorylation sites encode their sensitivity to starvation and rapamycin. Science (2013) 2.71
NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res (2007) 2.69
The combined status of ATM and p53 link tumor development with therapeutic response. Genes Dev (2009) 2.56
Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate. EMBO J (2007) 2.48
Mutant p53 oncogenic functions are sustained by Plk2 kinase through an autoregulatory feedback loop. Cell Cycle (2011) 2.46
The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Nature (2013) 2.46
Structural determinants of 14-3-3 binding specificities and regulation of subcellular localization of 14-3-3-ligand complexes: a comparison of the X-ray crystal structures of all human 14-3-3 isoforms. Semin Cancer Biol (2006) 2.42
A global analysis of cross-talk in a mammalian cellular signalling network. Nat Cell Biol (2006) 2.39
Merlin, the product of the Nf2 tumor suppressor gene, is an inhibitor of the p21-activated kinase, Pak1. Mol Cell (2003) 2.23
Dynamic scaffolding in a G protein-coupled signaling system. Cell (2007) 2.22
A structural basis for 14-3-3sigma functional specificity. J Biol Chem (2005) 2.20
The transcriptional co-activator TAZ interacts differentially with transcriptional enhancer factor-1 (TEF-1) family members. Biochem J (2005) 2.15
Overview of the Alliance for Cellular Signaling. Nature (2002) 2.15
The spatial architecture of protein function and adaptation. Nature (2012) 2.14
Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3. Mol Cell (2005) 2.10
The phosphoinositide-binding protein p40phox activates the NADPH oxidase during FcgammaIIA receptor-induced phagocytosis. J Exp Med (2006) 2.03
Structural and functional versatility of the FHA domain in DNA-damage signaling by the tumor suppressor kinase Chk2. Mol Cell (2002) 1.99
TAZ interacts with TTF-1 and regulates expression of surfactant protein-C. J Biol Chem (2004) 1.98
Allosteric determinants in guanine nucleotide-binding proteins. Proc Natl Acad Sci U S A (2003) 1.91
A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PLoS Biol (2010) 1.90
Hot spots for allosteric regulation on protein surfaces. Cell (2011) 1.89
Polo-like kinase 1 creates the tension-sensing 3F3/2 phosphoepitope and modulates the association of spindle-checkpoint proteins at kinetochores. Curr Biol (2005) 1.88
TAZ promotes PC2 degradation through a SCFbeta-Trcp E3 ligase complex. Mol Cell Biol (2007) 1.86
Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1. Nat Struct Mol Biol (2009) 1.84
ROS fusion tyrosine kinase activates a SH2 domain-containing phosphatase-2/phosphatidylinositol 3-kinase/mammalian target of rapamycin signaling axis to form glioblastoma in mice. Cancer Res (2006) 1.80
DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization. Mol Cell (2010) 1.78
Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells. PLoS Biol (2009) 1.78
TAZ: a beta-catenin-like molecule that regulates mesenchymal stem cell differentiation. Cell Cycle (2006) 1.76
Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening. BMC Biochem (2005) 1.74
Polo-like kinase Cdc5 controls the local activation of Rho1 to promote cytokinesis. Science (2006) 1.73
Cytoplasmic localization of tristetraprolin involves 14-3-3-dependent and -independent mechanisms. J Biol Chem (2002) 1.67
A reversible gene-targeting strategy identifies synthetic lethal interactions between MK2 and p53 in the DNA damage response in vivo. Cell Rep (2013) 1.67
14-3-3 Proteins--a focus on cancer and human disease. J Mol Cell Cardiol (2004) 1.67
14-3-3 proteins, FHA domains and BRCT domains in the DNA damage response. DNA Repair (Amst) (2009) 1.66
14-3-3 proteins as signaling integration points for cell cycle control and apoptosis. Semin Cell Dev Biol (2011) 1.65
Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell (2008) 1.65
Phospho-Ser/Thr-binding domains: navigating the cell cycle and DNA damage response. Nat Rev Mol Cell Biol (2013) 1.62
Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Sci Signal (2011) 1.62
A high-throughput quantitative multiplex kinase assay for monitoring information flow in signaling networks: application to sepsis-apoptosis. Mol Cell Proteomics (2003) 1.61
A positive feedback loop couples Ras activation and CD44 alternative splicing. Genes Dev (2006) 1.60
A novel assay system implicates PtdIns(3,4)P(2), PtdIns(3)P, and PKC delta in intracellular production of reactive oxygen species by the NADPH oxidase. Mol Cell (2003) 1.59
Proteomic identification of 14-3-3zeta as a mitogen-activated protein kinase-activated protein kinase 2 substrate: role in dimer formation and ligand binding. Mol Cell Biol (2003) 1.53
14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma. Proc Natl Acad Sci U S A (2012) 1.51
Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel. Nat Chem Biol (2011) 1.49
Computational approaches for analyzing information flow in biological networks. Sci Signal (2012) 1.49
Exploiting synthetic lethal interactions for targeted cancer therapy. Cell Cycle (2009) 1.44
An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol (2010) 1.42
A coupled chemical-genetic and bioinformatic approach to Polo-like kinase pathway exploration. Chem Biol (2007) 1.42
The rhoptry proteins ROP18 and ROP5 mediate Toxoplasma gondii evasion of the murine, but not the human, interferon-gamma response. PLoS Pathog (2012) 1.41
Public knowledge, attitude and behavioural changes in an Indian population during the Influenza A (H1N1) outbreak. J Infect Dev Ctries (2009) 1.38
Distinct mechanisms act in concert to mediate cell cycle arrest. Proc Natl Acad Sci U S A (2009) 1.37
The NDR/LATS family kinase Cbk1 directly controls transcriptional asymmetry. PLoS Biol (2008) 1.33
Signal transduction pathway of TonB-dependent transporters. Proc Natl Acad Sci U S A (2006) 1.32
Systematic phosphorylation analysis of human mitotic protein complexes. Sci Signal (2011) 1.31
Validation of the p21-activated kinases as targets for inhibition in neurofibromatosis type 2. Cancer Res (2008) 1.31
Caged phosphopeptides reveal a temporal role for 14-3-3 in G1 arrest and S-phase checkpoint function. Nat Biotechnol (2004) 1.26
The Polo-box domain: a molecular integrator of mitotic kinase cascades and Polo-like kinase function. Cell Cycle (2004) 1.23
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Functional dynamics of Polo-like kinase 1 at the centrosome. Mol Cell Biol (2009) 1.21
Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress. Mol Syst Biol (2012) 1.20
SIRT1 shows no substrate specificity in vitro. J Biol Chem (2005) 1.20
Identification of high affinity polo-like kinase 1 (Plk1) polo-box domain binding peptides using oxime-based diversification. ACS Chem Biol (2012) 1.16
Impaired SHP2-mediated extracellular signal-regulated kinase activation contributes to gefitinib sensitivity of lung cancer cells with epidermal growth factor receptor-activating mutations. Cancer Res (2010) 1.16