High-throughput analysis of peptide-binding modules

Annotator: Postprocessing Software for Generating Function-based Signatures from Quantitative Mass Spectrometry

(2012) Juliesta E. Sylvester et al.   JOURNAL OF PROTEOME RESEARCH

The protein interaction network mediated by human SH3 domains

(2011) Martina Carducci et al.   BIOTECHNOLOGY ADVANCES

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

A Conserved Residue in the Yeast Bem1p SH3 Domain Maintains the High Level of Binding Specificity Required for Function

(2011) Maryna Gorelik et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteomic Screening Method for Phosphopeptide Motif Binding Proteins Using Peptide Libraries

(2011) Heather R. Christofk et al.   JOURNAL OF PROTEOME RESEARCH

Beyond natural antibodies: the power of in vitro display technologies

(2011) Andrew R M Bradbury et al.   NATURE BIOTECHNOLOGY

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

Deciphering arginine methylation: Tudor tells the tale

(2011) Chen Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Inhibition of PI3K binding to activators by serine phosphorylation of PI3K regulatory subunit p85  Src homology-2 domains

(2011) J. Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The SH2 Domain-Containing Proteins in 21 Species Establish the Provenance and Scope of Phosphotyrosine Signaling in Eukaryotes

(2011) B. A. Liu et al.   Science Signaling

Predicting conserved protein motifs with Sub-HMMs

(2010) Kevin Horan et al.   BMC BIOINFORMATICS

A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

(2010) Nicolas Lenfant et al.   BMC GENOMICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Recognition and Specificity Determinants of the Human Cbx Chromodomains

(2010) Lilia Kaustov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy−Entropy Compensation in SH2−Ligand Binding

(2010) Joshua M. Ward et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SH2 Domains Recognize Contextual Peptide Sequence Information to Determine Selectivity

(2010) Bernard A. Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of lysine succinylation as a new post-translational modification

(2010) Zhihong Zhang et al.   Nature Chemical Biology

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition

(2010) Jaclyn R. Gareau et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Molecular mechanisms in signal transduction at the membrane

(2010) Jay T Groves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Characterizing Tyrosine Phosphorylation Signaling in Lung Cancer Using SH2 Profiling

(2010) Kazuya Machida et al.   PLoS One

Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens

(2010) Simona Panni et al.   PROTEOMICS

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Structure/Function Implications in a Dynamic Complex of the Intrinsically Disordered Sic1 with the Cdc4 Subunit of an SCF Ubiquitin Ligase

(2010) Tanja Mittag et al.   STRUCTURE

Genomic and structural aspects of protein evolution

(2009) Cyrus Chothia et al.   BIOCHEMICAL JOURNAL

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

The Selectivity of Receptor Tyrosine Kinase Signaling Is Controlled by a Secondary SH2 Domain Binding Site

(2009) Jae Hyun Bae et al.   CELL

Dissecting protein function and signaling using protein microarrays

(2009) Alejandro Wolf-Yadlin et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

14-3-3 proteins, FHA domains and BRCT domains in the DNA damage response

(2009) Duaa H. Mohammad et al.   DNA REPAIR

Array MAPPIT: High-Throughput Interactome Analysis in Mammalian Cells

(2009) Sam Lievens et al.   JOURNAL OF PROTEOME RESEARCH

Systems-level interactions between insulin–EGF networks amplify mitogenic signaling

(2009) Nikolay Borisov et al.   Molecular Systems Biology

Ubiquitin-binding domains — from structures to functions

(2009) Ivan Dikic et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cell Signaling in Space and Time: Where Proteins Come Together and When They're Apart

(2009) J. D. Scott et al.   SCIENCE

Rapid Evolution of Functional Complexity in a Domain Family

(2009) A. Ernst et al.   Science Signaling

Eukaryotic Protein Domains as Functional Units of Cellular Evolution

(2009) J. Jin et al.   Science Signaling

Mammalian two-hybrids come of age

(2009) Sam Lievens et al.   TRENDS IN BIOCHEMICAL SCIENCES

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

(2009) Raffi Tonikian et al.   PLOS BIOLOGY

Pfam 10 years on: 10 000 families and still growing

(2008) S. J. Sammut et al.   BRIEFINGS IN BIOINFORMATICS

High-order combination effects and biological robustness

(2008) Joseph Lehár et al.   Molecular Systems Biology

Membrane-dependent signal integration by the Ras activator Son of sevenless

(2008) Jodi Gureasko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Contextual Specificity in Peptide-Mediated Protein Interactions

(2008) Amelie Stein et al.   PLoS One

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

(2008) M. E. Sardiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome wide analysis of pathogenic SH2 domain mutations

(2008) Ilkka Lappalainen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Binding specificity of SH2 domains: Insight from free energy simulations

(2008) Wenxun Gan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics

(2008) C. J. Bashor et al.   SCIENCE

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY