Published in J Biol Chem on June 08, 2006
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Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol (2012) 2.14
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Computer-aided design of functional protein interactions. Nat Chem Biol (2009) 1.73
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High affinity small protein inhibitors of human chymotrypsin C (CTRC) selected by phage display reveal unusual preference for P4' acidic residues. J Biol Chem (2011) 1.18
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Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. PLoS One (2011) 1.04
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
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Monospecific inhibitors show that both mannan-binding lectin-associated serine protease-1 (MASP-1) and -2 Are essential for lectin pathway activation and reveal structural plasticity of MASP-2. J Biol Chem (2012) 0.94
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Fine mapping of the sequence requirements for binding of beta-lactamase inhibitory protein (BLIP) to TEM-1 beta-lactamase using a genetic screen for BLIP function. J Mol Biol (2009) 0.83
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A computational framework to empower probabilistic protein design. Bioinformatics (2008) 0.82
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Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment. BMC Biochem (2013) 0.79
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Low-stringency selection of TEM1 for BLIP shows interface plasticity and selection for faster binders. Proc Natl Acad Sci U S A (2016) 0.75
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Engineered Autonomous Human Variable Domains. Curr Pharm Des (2016) 0.75
Construction of Structural Mimetics of the Thyrotropin Receptor Intracellular Domain. Biophys J (2016) 0.75
Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity. Proc Natl Acad Sci U S A (2008) 17.41
Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature (2010) 16.12
Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell (2008) 5.37
A specificity map for the PDZ domain family. PLoS Biol (2008) 3.16
High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol (2007) 2.88
A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design. Nat Biotechnol (2005) 2.51
Crystal structure of full-length KcsA in its closed conformation. Proc Natl Acad Sci U S A (2009) 2.35
Regulation of a late phase of T cell polarity and effector functions by Crtam. Cell (2008) 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
Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide. Nature (2013) 2.14
High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. J Mol Biol (2004) 2.14
Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation. Science (2012) 1.92
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
Structural basis for the activity of drugs that inhibit phosphodiesterases. Structure (2004) 1.84
Crystal structures of proto-oncogene kinase Pim1: a target of aberrant somatic hypermutations in diffuse large cell lymphoma. J Mol Biol (2005) 1.79
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol (2009) 1.78
Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis. Nat Chem Biol (2006) 1.68
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
X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers. J Am Chem Soc (2008) 1.64
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
Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activity. Mol Cell Biol (2004) 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
Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain. J Biol Chem (2002) 1.49
Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat Protoc (2007) 1.49
Tyrosine 813 is a site of JAK2 autophosphorylation critical for activation of JAK2 by SH2-B beta. Mol Cell Biol (2004) 1.46
A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. J Mol Biol (2008) 1.45
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
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
Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol Biosyst (2010) 1.35
Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling. Biochem J (2010) 1.34
Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis. J Mol Biol (2002) 1.33
Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Sci (2007) 1.31
Bivalent antibody phage display mimics natural immunoglobulin. J Immunol Methods (2004) 1.30
Definition of the consensus motif recognized by gamma-adaptin ear domains. J Biol Chem (2003) 1.29
CDR-H3 diversity is not required for antigen recognition by synthetic antibodies. J Mol Biol (2012) 1.27
Comprehensive analysis of the factors contributing to the stability and solubility of autonomous human VH domains. J Biol Chem (2007) 1.26
Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code. J Mol Biol (2005) 1.26
Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins. Nat Struct Mol Biol (2011) 1.23
Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods. Protein Sci (2009) 1.20
Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold. Protein Sci (2008) 1.20
A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat Struct Mol Biol (2010) 1.18
Mechanism of activation gating in the full-length KcsA K+ channel. Proc Natl Acad Sci U S A (2011) 1.15
The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol (2011) 1.14
Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope. J Mol Biol (2007) 1.13
The functional capacity of the natural amino acids for molecular recognition. Mol Biosyst (2010) 1.12
Phosphorylation of JAK2 at serine 523: a negative regulator of JAK2 that is stimulated by growth hormone and epidermal growth factor. Mol Cell Biol (2006) 1.12
Structure of bistramide A-actin complex at a 1.35 angstroms resolution. J Am Chem Soc (2006) 1.10
Contributions of CDR3 to V H H domain stability and the design of monobody scaffolds for naive antibody libraries. J Mol Biol (2003) 1.08
The crystal structure of a quercetin 2,3-dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s). Biochemistry (2005) 1.07
Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain. Protein Sci (2007) 1.06
Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods (2012) 1.06
The functional binding epitope of a high affinity variant of human growth hormone mapped by shotgun alanine-scanning mutagenesis: insights into the mechanisms responsible for improved affinity. J Mol Biol (2003) 1.06
T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment. PLoS One (2012) 1.05
An engineered substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells. Proc Natl Acad Sci U S A (2009) 1.04
Synthetic human monoclonal antibodies toward staphylococcal enterotoxin B (SEB) protective against toxic shock syndrome. J Biol Chem (2012) 1.04
The role of protein dynamics in increasing binding affinity for an engineered protein-protein interaction established by H/D exchange mass spectrometry. Biochemistry (2006) 1.01
Interaction domains of Sos1/Grb2 are finely tuned for cooperative control of embryonic stem cell fate. Cell (2013) 0.99
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
Total chemical synthesis and X-ray crystal structure of a protein diastereomer: [D-Gln 35]ubiquitin. Angew Chem Int Ed Engl (2005) 0.99
KIF14 negatively regulates Rap1a-Radil signaling during breast cancer progression. J Cell Biol (2012) 0.99
X-ray structure of native scorpion toxin BmBKTx1 by racemic protein crystallography using direct methods. J Am Chem Soc (2009) 0.99
Site2 binding energetics of the regulatory step of growth hormone-induced receptor homodimerization. Protein Sci (2003) 0.98
Exploring and designing protein function with restricted diversity. Curr Opin Chem Biol (2007) 0.97
Two synthetic antibodies that recognize and neutralize distinct proteolytic forms of the ebola virus envelope glycoprotein. Chembiochem (2012) 0.97
Synthetic antibodies with a human framework that protect mice from lethal Sudan ebolavirus challenge. ACS Chem Biol (2014) 0.97
Submitting antibodies to binding arbitration. Nat Chem Biol (2008) 0.96
Dissecting the binding energy epitope of a high-affinity variant of human growth hormone: cooperative and additive effects from combining mutations from independently selected phage display mutagenesis libraries. Biochemistry (2004) 0.95
The high- and low-affinity receptor binding sites of growth hormone are allosterically coupled. Proc Natl Acad Sci U S A (2004) 0.95
Determination of the energetics governing the regulatory step in growth hormone-induced receptor homodimerization. Proc Natl Acad Sci U S A (2003) 0.95
Charged and hydrophobic surfaces on the a chain of shiga-like toxin 1 recognize the C-terminal domain of ribosomal stalk proteins. PLoS One (2012) 0.94
SH3 interactome conserves general function over specific form. Mol Syst Biol (2013) 0.94
Shotgun alanine scanning shows that growth hormone can bind productively to its receptor through a drastically minimized interface. J Biol Chem (2005) 0.94
Alternative views of functional protein binding epitopes obtained by combinatorial shotgun scanning mutagenesis. Protein Sci (2005) 0.94
A structure-based database of antibody variable domain diversity. J Mol Biol (2005) 0.94
MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics (2010) 0.93
Superbinder SH2 domains act as antagonists of cell signaling. Sci Signal (2012) 0.92
Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine. J Mol Biol (2010) 0.91
Design and pharmacology of a highly specific dual FMS and KIT kinase inhibitor. Proc Natl Acad Sci U S A (2013) 0.91
Evolving specificity from variability for protein interaction domains. Trends Biochem Sci (2011) 0.91
Intramolecular cooperativity in a protein binding site assessed by combinatorial shotgun scanning mutagenesis. J Mol Biol (2005) 0.90
Rapid identification of small binding motifs with high-throughput phage display: discovery of peptidic antagonists of IGF-1 function. Chem Biol (2002) 0.90
Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography. Proc Natl Acad Sci U S A (2012) 0.89
Engineering and analysis of peptide-recognition domain specificities by phage display and deep sequencing. Methods Enzymol (2013) 0.89
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. Nucleic Acids Res (2011) 0.89
Recombinant antibodies and in vitro selection technologies. Methods Mol Biol (2012) 0.88
Studying binding specificities of peptide recognition modules by high-throughput phage display selections. Methods Mol Biol (2011) 0.88
A short DNA aptamer that recognizes TNFα and blocks its activity in vitro. ACS Chem Biol (2012) 0.87
Selective and brain-permeable polo-like kinase-2 (Plk-2) inhibitors that reduce α-synuclein phosphorylation in rat brain. ChemMedChem (2013) 0.87