Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin

PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems

(2016) Markus Fleck et al.   Journal of Chemical Theory and Computation

Universal features of fluctuations in globular proteins

(2016) Burak Erman   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions

(2016) Sezen Vatansever et al.   Scientific Reports

Coupled binding–bending–folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations

(2015) Arjan van der Vaart   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods

(2015) Summer Kassem et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins

(2015) Montserrat Barbany et al.   PLoS One

PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites

(2014) Alejandro Panjkovich et al.   BIOINFORMATICS

Recent computational advances in the identification of allosteric sites in proteins

(2014) Shaoyong Lu et al.   DRUG DISCOVERY TODAY

Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer

(2014) Liqun Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

A Unified View of “How Allostery Works”

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

Emerging computational approaches for the study of protein allostery

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

Quantification of Drive-Response Relationships Between Residues During Protein Folding

(2013) Yifei Qi et al.   Journal of Chemical Theory and Computation

CENCALC: A computational tool for conformational entropy calculations from molecular simulations

(2013) Ernesto Suárez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2013) Cihan Kaya et al.   NUCLEIC ACIDS RESEARCH

Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors

(2013) Juan R. Perilla et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A fast approximate method of identifying paths of allosteric communication in proteins

(2013) Burak Erman   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Importance of local interactions for the stability of inhibitory helix 1 in apo Ets-1

(2012) Aleksandra Karolak et al.   BIOPHYSICAL CHEMISTRY

The role of allostery in the ubiquitin–proteasome system

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

Multibody local approximation: Application to conformational entropy calculations on biomolecules

(2012) Ernesto Suárez et al.   JOURNAL OF CHEMICAL PHYSICS

Balanced and Bias-Corrected Computation of Conformational Entropy Differences for Molecular Trajectories

(2012) Jorge Numata et al.   Journal of Chemical Theory and Computation

Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation

(2012) Bracken M. King et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Investigating Allostery in Molecular Recognition: Insights from a Computational Study of Multiple Antibody–Antigen Complexes

(2012) Dario Corrada et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Kinetics of Conformational Sampling in Ubiquitin

(2011) David Ban et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Importance of Domain Closure for the Autoactivation of ERK2

(2011) Daniel Barr et al.   BIOCHEMISTRY

Independent Interactions of Ubiquitin-Binding Domains in a Ubiquitin-Mediated Ternary Complex

(2011) Thomas P. Garner et al.   BIOCHEMISTRY

Entropy Calculations of Single Molecules by Combining the Rigid–Rotor and Harmonic-Oscillator Approximations with Conformational Entropy Estimations from Molecular Dynamics Simulations

(2011) Ernesto Suárez et al.   Journal of Chemical Theory and Computation

Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition

(2011) R. Bryn Fenwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting Interaction Sites from the Energetics of Isolated Proteins: A New Approach to Epitope Mapping

(2010) Guido Scarabelli et al.   BIOPHYSICAL JOURNAL

ASD: a comprehensive database of allosteric proteins and modulators

(2010) Z. Huang et al.   NUCLEIC ACIDS RESEARCH

Extracting the Causality of Correlated Motions from Molecular Dynamics Simulations

(2009) Hiqmet Kamberaj et al.   BIOPHYSICAL JOURNAL

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

(2009) Christopher L. McClendon et al.   Journal of Chemical Theory and Computation

Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods

(2008) Vladimir Hnizdo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY