Uncovering new aspects of protein interactions through analysis of specificity landscapes in peptide recognition domains

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets

(2012) TaeHyung Kim et al.   NUCLEIC ACIDS RESEARCH

Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains

(2012) Stefano Mostarda et al.   PLoS Computational Biology

A Dynamic View of Domain-Motif Interactions

(2012) Eyal Akiva et al.   PLoS Computational Biology

Rewiring of PDZ Domain-Ligand Interaction Network Contributed to Eukaryotic Evolution

(2012) Jinho Kim et al.   PLoS Genetics

The Cdc42-associated kinase ACK1 is not autoinhibited but requires Src for activation

(2011) Wing Chan et al.   BIOCHEMICAL JOURNAL

Phage display can select over-hydrophobic sequences that may impair prediction of natural domain–peptide interactions

(2011) Katja Luck et al.   BIOINFORMATICS

Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps

(2011) Kevin Y Yip et al.   BMC BIOLOGY

The Src Homology 3 Domain Is Required for Junctional Adhesion Molecule Binding to the Third PDZ Domain of the Scaffolding Protein ZO-1

(2011) Julian Nomme et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The multiple-specificity landscape of modular peptide recognition domains

(2011) D. Gfeller et al.   Molecular Systems Biology

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

(2011) Stuart A. Sievers et al.   NATURE

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

ELM--the database of eukaryotic linear motifs

(2011) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences

(2011) T. Mi et al.   NUCLEIC ACIDS RESEARCH

Large-scale characterization of peptide-MHC binding landscapes with structural simulations

(2011) C. Yanover 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

Spatial Exclusivity Combined with Positive and Negative Selection of Phosphorylation Motifs Is the Basis for Context-Dependent Mitotic Signaling

(2011) J. Alexander et al.   Science Signaling

Evolution of biological interaction networks: from models to real data

(2011) Mark GF Sun et al.   GENOME BIOLOGY

Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling

(2010) Tsutomu Oka et al.   BIOCHEMICAL JOURNAL

A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain–peptide interaction from primary sequence

(2010) Xiaojian Shao et al.   BIOINFORMATICS

MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains

(2010) Hugo YK Lam et al.   BMC BIOINFORMATICS

Evidence for a TCR Affinity Threshold Delimiting Maximal CD8 T Cell Function

(2010) D. A. Schmid et al.   JOURNAL OF IMMUNOLOGY

Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains

(2010) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

The Tiam1 PDZ Domain Couples to Syndecan1 and Promotes Cell–Matrix Adhesion

(2010) Tyson R. Shepherd et al.   JOURNAL OF MOLECULAR BIOLOGY

Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing

(2010) Andreas Ernst et al.   Molecular BioSystems

A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae

(2010) Oriol Gallego et al.   Molecular Systems Biology

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Quantifying protein–protein interactions in high throughput using protein domain microarrays

(2010) Alexis Kaushansky et al.   Nature Protocols

Determining the specificity of protein–DNA interactions

(2010) Gary D. Stormo et al.   NATURE REVIEWS GENETICS

Specificity landscapes of DNA binding molecules elucidate biological function

(2010) C. D. Carlson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-based prediction of protein-peptide specificity in rosetta

(2010) Christopher A. King et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs

(2010) J. Mok et al.   Science Signaling

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors

(2010) Thomas C. Whisenant et al.   PLoS Computational Biology

Extensions of PDZ domains as important structural and functional elements

(2010) Conan K. Wang et al.   Protein & Cell

Structure of the first PDZ domain of human PSD-93

(2009) Monica Fiorentini et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Structure-Based Prediction of the Saccharomyces cerevisiae SH3–Ligand Interactions

(2009) Gregorio Fernandez-Ballester et al.   JOURNAL OF MOLECULAR BIOLOGY

Design of protein-interaction specificity gives selective bZIP-binding peptides

(2009) Gevorg Grigoryan et al.   NATURE

Detection of protein–protein interactions by ribosome display and protein in situ immobilisation

(2009) Mingyue He et al.   New Biotechnology

Using genome-wide measurements for computational prediction of SH2–peptide interactions

(2009) Zeba Wunderlich et al.   NUCLEIC ACIDS RESEARCH

Hidden dynamic allostery in a PDZ domain

(2009) C. M. Petit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Positive Selection of Tyrosine Loss in Metazoan Evolution

(2009) C. S. H. Tan et al.   SCIENCE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

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

(2009) Raffi Tonikian et al.   PLOS BIOLOGY

Modified Peptides as Potent Inhibitors of the Postsynaptic Density-95/N-Methyl-d-Aspartate Receptor Interaction

(2008) Anders Bach et al.   JOURNAL OF MEDICINAL CHEMISTRY

Characterization of Domain–Peptide Interaction Interface: A Case Study on the Amphiphysin-1 SH3 Domain

(2008) Tingjun Hou et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting PDZ domain–peptide interactions from primary sequences

(2008) Jiunn R Chen et al.   NATURE BIOTECHNOLOGY

Contextual Specificity in Peptide-Mediated Protein Interactions

(2008) Amelie Stein et al.   PLoS One

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY

Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm

(2008) Ignacio E. Sánchez et al.   PLoS Computational Biology