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

The multiple-specificity landscape of modular peptide recognition domains

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

Putting into Practice Domain-Linear Motif Interaction Predictions for Exploration of Protein Networks

(2011) Katja Luck et al.   PLoS One

Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

(2011) Z. Nevin Gerek et al.   PLoS Computational Biology

Distal Interactions within the par3−VE-Cadherin Complex,

(2010) Robert C. Tyler et al.   BIOCHEMISTRY

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

(2010) Pär Bjelkmar et al.   Journal of Chemical Theory and Computation

Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

(2010) Michele Seeber et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Local Transition Gradients Indicating the Global Attributes of Protein Energy Landscapes

(2010) Francesco Rao   Journal of Physical Chemistry Letters

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

(2010) Carl Diehl et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein dynamics investigated by inherent structure analysis

(2010) F. Rao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensions of PDZ domains as important structural and functional elements

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

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Dictionary for Protein Side-Chain Entropies from NMR Order Parameters

(2009) Da-Wei Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Pfam protein families database

(2009) Robert D. Finn 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

Rapid Evolution of Functional Complexity in a Domain Family

(2009) A. Ernst et al.   Science Signaling

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

(2009) Diego Prada-Gracia et al.   PLoS Computational Biology

Par-3-mediated Junctional Localization of the Lipid Phosphatase PTEN Is Required for Cell Polarity Establishment

(2008) Wei Feng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

SMART 6: recent updates and new developments

(2008) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY