Machine learning approaches to evaluate correlation patterns in allosteric signaling: A case study of the PDZ2 domain

Stimulation of Nipah Fusion: Small Intradomain Changes Trigger Extensive Interdomain Rearrangements

(2016) Priyanka Dutta et al.   BIOPHYSICAL JOURNAL

Protein Allostery and Conformational Dynamics

(2016) Jingjing Guo et al.   CHEMICAL REVIEWS

Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation

(2015) Kateri H. DuBay et al.   ACCOUNTS OF CHEMICAL RESEARCH

Water Dynamics at Protein–Protein Interfaces: Molecular Dynamics Study of Virus–Host Receptor Complexes

(2014) Priyanka Dutta et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning

(2014) Sameer Varma et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Unified View of “How Allostery Works”

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

Quantitative Comparison of Conformational Ensembles

(2012) Kevin C. Wolfe et al.   Entropy

Comparing Conformational Ensembles Using the Kullback–Leibler Divergence Expansion

(2012) Christopher L. McClendon et al.   Journal of Chemical Theory and Computation

Quantifying Changes in Intrinsic Molecular Motion Using Support Vector Machines

(2012) Ralph E. Leighty et al.   Journal of Chemical Theory and Computation

Recent advances in computational protein design

(2011) Robert J Pantazes et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Allosteric Communication in Cysteinyl tRNA Synthetase

(2011) Amit Ghosh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

On the role of frustration in the energy landscapes of allosteric proteins

(2011) Diego U. Ferreiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Manipulation of Conformational Change in Proteins by Single-Residue Perturbations

(2010) C. Atilgan et al.   BIOPHYSICAL JOURNAL

PDZ domains and their binding partners: structure, specificity, and modification

(2010) Ho-Jin Lee et al.   Cell Communication and Signaling

Large conformational changes in proteins: signaling and other functions

(2010) Barry J Grant et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein dynamics and allostery: an NMR view

(2010) Shiou-Ru Tzeng et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Engineered allosteric activation of kinases in living cells

(2010) Andrei V Karginov et al.   NATURE BIOTECHNOLOGY

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conservation of Side-Chain Dynamics Within a Protein Family

(2009) Anthony B. Law et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computer-aided design of functional protein interactions

(2009) Daniel J Mandell et al.   Nature Chemical Biology

Similarity Measures for Protein Ensembles

(2009) Kresten Lindorff-Larsen et al.   PLoS One

Protein elastic network models and the ranges of cooperativity

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis

(2009) Wolfram Stacklies et al.   PLoS Computational Biology

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein

(2009) Canan Atilgan 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

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

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

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE

Deriving protein dynamical properties from weighted protein contact number

(2008) Chih-Peng Lin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation