High-throughput methods for identification of protein-protein interactions involving short linear motifs

The ABBA Motif Binds APC/C Activators and Is Shared by APC/C Substrates and Regulators

(2015) Barbara Di Fiore et al.   DEVELOPMENTAL CELL

Versatile communication strategies among tandem WW domain repeats

(2015) Emma Joy Dodson et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

SORTCERY—A High–Throughput Method to Affinity Rank Peptide Ligands

(2015) Lothar “Luther” Reich et al.   JOURNAL OF MOLECULAR BIOLOGY

Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants

(2015) Santiago J. Carmona et al.   MOLECULAR & CELLULAR PROTEOMICS

Application guide for omics approaches to cell signaling

(2015) Zhong Yao et al.   Nature Chemical Biology

Quantifying domain-ligand affinities and specificities by high-throughput holdup assay

(2015) Renaud Vincentelli et al.   NATURE METHODS

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

(2014) Michael E. Birnbaum et al.   CELL

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

(2014) Brett W. Engelmann et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteome-wide Epitope Mapping of Antibodies Using Ultra-dense Peptide Arrays

(2014) Björn Forsström et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?

(2014) Bora Uyar et al.   Molecular BioSystems

A Million Peptide Motifs for the Molecular Biologist

(2014) Peter Tompa et al.   MOLECULAR CELL

Identification of target-binding peptide motifs by high-throughput sequencing of phage-selected peptides

(2014) Inmaculada Rentero Rebollo et al.   NUCLEIC ACIDS RESEARCH

Fast and Accurate Discovery of Degenerate Linear Motifs in Protein Sequences

(2014) Abdellali Kelil et al.   PLoS One

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

(2014) Y. Ivarsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins

(2014) Joe DeBartolo et al.   PLoS Computational Biology

Interaction Analysis through Proteomic Phage Display

(2014) Gustav N. Sundell et al.   Biomed Research International

DoReMi: context-based prioritization of linear motif matches

(2014) Heiko Horn et al.   PeerJ

Structures and target recognition modes of PDZ domains: recurring themes and emerging pictures

(2013) Fei Ye et al.   BIOCHEMICAL JOURNAL

Marked by association: techniques for proximity-dependent labeling of proteins in eukaryotic cells

(2013) Kyle J. Roux   CELLULAR AND MOLECULAR LIFE SCIENCES

The Human PDZome: A Gateway to PSD95-Disc Large-Zonula Occludens (PDZ)-mediated Functions

(2013) Edwige Belotti et al.   MOLECULAR & CELLULAR PROTEOMICS

SH3 interactome conserves general function over specific form

(2013) X. Xin et al.   Molecular Systems Biology

The SH2 Domain Interaction Landscape

(2013) Michele Tinti et al.   Cell Reports

Interactome Mapping: Using Protein Microarray Technology to Reconstruct Diverse Protein Networks

(2013) Ijeoma Uzoma et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

Current advances in peptide and small molecule microarray technologies

(2012) Yu M Foong et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Motif switches: decision-making in cell regulation

(2012) Kim Van Roey et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Plasticity of PDZ domains in ligand recognition and signaling

(2012) Ylva Ivarsson   FEBS LETTERS

Synthetic peptide arrays for investigating protein interaction domains

(2012) Rudolf Volkmer et al.   FEBS LETTERS

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

Proteomics Strategy to Identify Substrates of LNX, a PDZ Domain-containing E3 Ubiquitin Ligase

(2012) Zhengguang Guo et al.   JOURNAL OF PROTEOME RESEARCH

Protein selection using yeast surface display

(2012) Nimish Gera et al.   METHODS

High-resolution Mapping of Linear Antibody Epitopes Using Ultrahigh-density Peptide Microarrays

(2012) Søren Buus et al.   MOLECULAR & CELLULAR PROTEOMICS

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

(2012) Norman E. Davey et al.   NUCLEIC ACIDS RESEARCH

Peptide Array X-Linking (PAX): A New Peptide-Protein Identification Approach

(2012) Hirokazu Okada et al.   PLoS One

High-throughput analysis of peptide-binding modules

(2012) Bernard A. Liu et al.   PROTEOMICS

Strategies for membrane interaction proteomics: No mass spectrometry required

(2012) Mandy H. Y. Lam et al.   PROTEOMICS

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

(2011) Katja Luck et al.   BIOINFORMATICS

Studying protein–protein interactions using peptide arrays

(2011) Chen Katz et al.   CHEMICAL SOCIETY REVIEWS

Split-protein systems: beyond binary protein–protein interactions

(2011) Sujan S Shekhawat et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Three-dimensional modeling of protein interactions and complexes is going ‘omics

(2011) Amelie Stein et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The multiple-specificity landscape of modular peptide recognition domains

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

Autoantigen discovery with a synthetic human peptidome

(2011) H Benjamin Larman et al.   NATURE BIOTECHNOLOGY

SLiMSearch 2.0: biological context for short linear motifs in proteins

(2011) N. E. Davey et al.   NUCLEIC ACIDS RESEARCH

ELM--the database of eukaryotic linear motifs

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

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

Recent advances in charting protein–protein interaction: mass spectrometry-based approaches

(2010) Anne-Claude Gavin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Determinants of BH3 Binding Specificity for Mcl-1 versus Bcl-xL

(2010) Sanjib Dutta et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2010) Alexis Kaushansky et al.   Nature Protocols

Rapid interactome profiling by massive sequencing

(2010) Roberto Di Niro et al.   NUCLEIC ACIDS RESEARCH

Transient Protein-Protein Interactions: Structural, Functional, and Network Properties

(2010) James R. Perkins et al.   STRUCTURE

Novel Peptide-Mediated Interactions Derived from High-Resolution 3-Dimensional Structures

(2010) Amelie Stein et al.   PLoS Computational Biology

Systematic Analysis of a Simple Adaptor Protein PDZK1: Ligand Identification, Interaction and Functional Prediction of Complex

(2009) Siqi Hu et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

A Decade of Yeast Surface Display Technology: Where Are We Now?

(2008) Eric Shusta et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Understanding eukaryotic linear motifs and their role in cell signaling and regulation

(2008) Francesca Diella   Frontiers in Bioscience-Landmark

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY