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

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

(2010) Hugo YK Lam et al.   BMC BIOINFORMATICS

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

(2010) J. Mok et al.   Science Signaling

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Enriching the viral–host interactomes with interactions mediated by SH3 domains

(2009) Martina Carducci et al.   AMINO ACIDS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Correlated Mutation Analysis on the Catalytic Domains of Serine/Threonine Protein Kinases

(2009) Feng Xu et al.   PLoS One

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

(2009) Thijs Beuming et al.   PROTEIN SCIENCE

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

Network medicine

(2008) Tony Pawson et al.   FEBS LETTERS

Predicting PDZ domain–peptide interactions from primary sequences

(2008) Jiunn R Chen et al.   NATURE BIOTECHNOLOGY

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt 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