Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery

Mapping Allostery through Computational Glycine Scanning and Correlation Analysis of Residue–Residue Contacts

(2015) Quentin R. Johnson et al.   BIOCHEMISTRY

Dynamics and thermodynamic properties of CXCL7 chemokine

(2015) Charles A. Herring et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Allosteric sites can be identified based on the residue-residue interaction energy difference

(2015) Xiaomin Ma et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins

(2015) Laleh Soltan Ghoraie et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Identifying Key Residues for Protein Allostery through Rigid Residue Scan

(2014) Robert Kalescky et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Principles of Allosteric Interactions in Cell Signaling

(2014) Ruth Nussinov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

(2014) Tong Li et al.   PLoS One

A Unified View of “How Allostery Works”

(2014) Chung-Jung Tsai et al.   PLoS Computational Biology

The Underappreciated Role of Allostery in the Cellular Network

(2013) Ruth Nussinov et al.   Annual Review of Biophysics

Emerging computational approaches for the study of protein allostery

(2013) Galen Collier et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Allostery in Disease and in Drug Discovery

(2013) Ruth Nussinov et al.   CELL

A Mixed Protein Structure Network and Elastic Network Model Approach to Predict the Structural Communication in Biomolecular Systems: The PDZ2 Domain from Tyrosine Phosphatase 1E As a Case Study

(2013) Francesco Raimondi et al.   Journal of Chemical Theory and Computation

Solution NMR and Computational Methods for Understanding Protein Allostery

(2013) Gregory Manley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues

(2013) Cihan Kaya et al.   NUCLEIC ACIDS RESEARCH

Surface Dynamics in Allosteric Regulation of Protein-Protein Interactions: Modulation of Calmodulin Functions by Ca2+

(2013) Yosef Y. Kuttner et al.   PLoS Computational Biology

Allostery and the Monod-Wyman-Changeux Model After 50 Years

(2012) Jean-Pierre Changeux   Annual Review of Biophysics

Structural and Energetic Basis of Allostery

(2012) Vincent J. Hilser et al.   Annual Review of Biophysics

The role of allostery in the ubiquitin–proteasome system

(2012) Jin Liu et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations

(2012) Peng Tao et al.   JOURNAL OF CHEMICAL PHYSICS

Allostery and cooperativity in Escherichia coli aspartate transcarbamoylase

(2011) Evan R. Kantrowitz   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Protein Allostery at the Solid–Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft

(2011) Yuchun Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Atomistic Kinetic Model for Population Shift and Allostery in Biomolecules

(2011) Dong Long et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E

(2010) Jun Zhang et al.   BIOCHEMISTRY

Allosteric Response Is both Conserved and Variable across Three CheY Orthologs

(2010) James M. Mottonen et al.   BIOPHYSICAL JOURNAL

Interaction Energy Based Protein Structure Networks

(2010) M.S. Vijayabaskar et al.   BIOPHYSICAL JOURNAL

Correlating allostery with rigidity

(2010) A. J. Rader et al.   Molecular BioSystems

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

A geometry-based generic predictor for catalytic and allosteric sites

(2010) S. Mitternacht et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

CHARMM: The biomolecular simulation program

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

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

(2009) Chung-Jung Tsai et al.   Molecular BioSystems

The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways

(2009) Antonio del Sol et al.   STRUCTURE

Computation of Conformational Coupling in Allosteric Proteins

(2009) Brian A. Kidd et al.   PLoS Computational Biology

Structure-Based Predictive Models for Allosteric Hot Spots

(2009) Omar N. A. Demerdash et al.   PLoS Computational Biology

Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis

(2009) Wolfram Stacklies et al.   PLoS Computational Biology

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins

(2009) Michael D. Daily et al.   PLoS Computational Biology

The Structure of a Mutant Insulin Uncouples Receptor Binding from Protein Allostery

(2008) Zhu-li Wan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An Allosteric Circuit in Caspase-1

(2008) Debajyoti Datta et al.   JOURNAL OF MOLECULAR BIOLOGY

Engineering Protein Allostery: 1.05 Å Resolution Structure and Enzymatic Properties of a Na+-activated Trypsin

(2008) Michael J. Page et al.   JOURNAL OF MOLECULAR BIOLOGY

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Allosteric regulation and catalysis emerge via a common route

(2008) Nina M Goodey et al.   Nature Chemical Biology

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE

Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis

(2008) Yifei Kong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS