Direct methods for computing single-molecule entropies from molecular simulations

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

(2013) John D. Chodera et al.   Annual Review of Biophysics

Accelerated Conformational Entropy Calculations Using Graphic Processing Units

(2013) Qian Zhang et al.   Journal of Chemical Information and Modeling

Absolute Free Energy of Binding and Entropy of the FKBP12-FK506 Complex: Effects of the Force Field

(2013) Ignacio J. General et al.   Journal of Chemical Theory and Computation

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

(2013) Samuel Genheden 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

Conformational Entropy of Intrinsically Disordered Protein

(2013) Song-Ho Chong et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Microscopic Insights into the NMR Relaxation-Based Protein Conformational Entropy Meter

(2013) Vignesh Kasinath et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Entropies of Adsorbed Molecules Exceed Expectations

(2013) J. F. Weaver   SCIENCE

The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation

(2012) A Joshua Wand   CURRENT OPINION IN STRUCTURAL BIOLOGY

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

(2012) Junmei Wang et al.   Journal of Chemical Information and Modeling

Multibody local approximation: Application to conformational entropy calculations on biomolecules

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

A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory

(2012) Ryan M. Richard et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic and Thermodynamic Signatures of Native and Non-Native Protein States with Application to the Improvement of Protein Structures

(2012) Da-Wei Li et al.   Journal of Chemical Theory and Computation

On the Contribution of Linear Correlations to Quasi-harmonic Conformational Entropy in Proteins

(2012) Anton A. Polyansky et al.   Journal of Chemical Theory and Computation

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

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

Exploring Residue Component Contributions to Dynamical Network Models of Allostery

(2012) Adam T. VanWart et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Calculation of Molecular Entropies Using Temperature Integration

(2012) Kim Sharp   Journal of Chemical Theory and Computation

Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance-dependent dielectric model

(2012) Hannes Kopitz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Alternative Interdomain Configurations of the Full-Length MMP-2 Enzyme Explored by Molecular Dynamics Simulations

(2012) Natalia Díaz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation

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

A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences

(2012) Victor Ovchinnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Entropies of Adsorbed Molecules

(2012) Charles T. Campbell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Will molecular dynamics simulations of proteins ever reach equilibrium?

(2012) Samuel Genheden et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding

(2012) A. T. Fenley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Equilibrium Sampling in Biomolecular Simulations

(2011) Daniel M. Zuckerman   Annual Review of Biophysics

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

(2011) Mark S. Gordon et al.   CHEMICAL REVIEWS

Distinguishability in Entropy Calculations: Chemical Reactions, Conformational and Residual Entropy

(2011) Ernesto Suárez   Entropy

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

Evaluation of protein-ligand binding free energy focused on its entropic components

(2011) Shuntaro Chiba et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Calculation of Configurational Entropy with a Boltzmann–Quasiharmonic Model: The Origin of High-Affinity Protein–Ligand Binding

(2011) Kyle W. Harpole et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Behind the folding funnel diagram

(2011) Martin Karplus   Nature Chemical Biology

Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature

(2011) Phuong H. Nguyen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Thermodynamic and Differential Entropy under a Change of Variables

(2010) Vladimir Hnizdo et al.   Entropy

Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian

(2010) S. Wlodek et al.   Journal of Chemical Theory and Computation

Configurational Entropy Reallocation and Complex Loop Dynamics of the Mosquito-Stage Pvs25 Protein Complexed with the Fab Fragment of the Malaria Transmission Blocking Antibody 2A8

(2010) Athanassios Stavrakoudis et al.   Journal of Chemical Theory and Computation

Symmetry Numbers for Rigid, Flexible, and Fluxional Molecules: Theory and Applications†

(2010) Michael K. Gilson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets

(2009) Bracken M. King et al.   BIOINFORMATICS

Correlated Motions and Interactions at the Onset of the DNA-Induced Partial Unfolding of Ets-1

(2009) Hiqmet Kamberaj et al.   BIOPHYSICAL JOURNAL

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

Thermodynamic Properties of Liquid Water: An Application of a Nonparametric Approach to Computing the Entropy of a Neat Fluid

(2009) Lingle Wang et al.   Journal of Chemical Theory and Computation

Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties

(2009) Riccardo Baron et al.   Journal of Chemical Theory and Computation

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

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

Calculation of Proteins’ Total Side-Chain Torsional Entropy and Its Influence on Protein–Ligand Interactions

(2009) Kateri H. DuBay et al.   JOURNAL OF MOLECULAR BIOLOGY

Configurational Entropy in Protein–Peptide Binding:

(2009) Benjamin J. Killian et al.   JOURNAL OF MOLECULAR BIOLOGY

Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers

(2009) M. Cecchini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Absolute Free Energy and Entropy of a Mobile Loop of the Enzyme Acetylcholinesterase

(2009) Mihail Mihailescu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects

(2009) Nidhi Singh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces

(2009) Ulf Hensen et al.   PHYSICAL REVIEW E

In silicoRelationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides

(2009) Da-Wei Li et al.   PHYSICAL REVIEW LETTERS

Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations

(2009) Natalia Díaz et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

An improved method to predict the entropy term with the MM/PBSA approach

(2008) Jacob Kongsted et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases

(2008) Ileana Stoica et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Side-Chain Dynamics and Residual Conformational Entropy

(2008) Nikola Trbovic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY