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

Interaction prediction and classification of PDZ domains

(2010) Sibel Kalyoncu et al.   BMC BIOINFORMATICS

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

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

(2010) Andreas Ernst et al.   Molecular BioSystems

Domain Interaction Footprint: a multi-classification approach to predict domain–peptide interactions

(2009) Christian Schillinger et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

T7 phage display as a method of peptide ligand discovery for PDZ domain proteins

(2009) Sudhir C. Sharma et al.   BIOPOLYMERS

Competitively selected protein ligands pay their increase in specificity by a decrease in affinity

(2009) Silke Hoffmann et al.   Molecular BioSystems

High-energy water sites determine peptide binding affinity and specificity of PDZ domains

(2009) Thijs Beuming et al.   PROTEIN SCIENCE

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

(2008) Francesca Diella   Frontiers in Bioscience-Landmark

Predicting PDZ domain–peptide interactions from primary sequences

(2008) Jiunn R Chen et al.   NATURE BIOTECHNOLOGY

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY