Understanding conformational entropy in small molecules
The calculation of the entropy of flexible molecules can be challenging, since the number of
possible conformers can grow exponentially with molecule size and many low-energy …
possible conformers can grow exponentially with molecule size and many low-energy …
Entropy calculations of single molecules by combining the rigid–rotor and harmonic-oscillator approximations with conformational entropy estimations from molecular …
As shown by previous theoretical and computational work, absolute entropies of small
molecules that populate different conformers can be predicted accurately on the basis of the …
molecules that populate different conformers can be predicted accurately on the basis of the …
Towards understanding solvation effects on the conformational entropy of non-rigid molecules
The absolute molecular entropy is a fundamental quantity for the accurate description of
thermodynamic properties. For non-rigid molecules, a substantial part of the entropy can be …
thermodynamic properties. For non-rigid molecules, a substantial part of the entropy can be …
The dynameomics entropy dictionary: a large-scale assessment of conformational entropy across protein fold space
Molecular dynamics (MD) simulations contain considerable information with regard to the
motions and fluctuations of a protein, the magnitude of which can be used to estimate …
motions and fluctuations of a protein, the magnitude of which can be used to estimate …
Direct methods for computing single‐molecule entropies from molecular simulations
D Suárez, N Díaz - Wiley Interdisciplinary Reviews …, 2015 - Wiley Online Library
Assessing the actual role of entropic forces in controlling both the stability and activity of
flexible molecules and macromolecules is a theoretical challenge that is gradually gaining …
flexible molecules and macromolecules is a theoretical challenge that is gradually gaining …
Evaluation of Configurational Entropy Methods from Peptide Folding− Unfolding Simulation
DW Li, M Khanlarzadeh, J Wang, S Huo… - The Journal of …, 2007 - ACS Publications
A 4-μs molecular dynamics simulation of the second β-hairpin of the B1 domain of
streptococcal protein G is used to characterize the free energy surface and to evaluate …
streptococcal protein G is used to characterize the free energy surface and to evaluate …
Calculation of absolute molecular entropies and heat capacities made simple
We propose a fully-automated composite scheme for the accurate and numerically stable
calculation of molecular entropies by efficiently combining density-functional theory (DFT) …
calculation of molecular entropies by efficiently combining density-functional theory (DFT) …
Conformational entropies and order parameters: convergence, reproducibility, and transferability
Conformational entropy provides major contributions to protein folding and functions, such
as ligand binding, making it a potentially important driver of biologically relevant processes …
as ligand binding, making it a potentially important driver of biologically relevant processes …
Torsional anharmonicity in the conformational thermodynamics of flexible molecules
TF Miller III*, DC Clary - Molecular Physics, 2005 - Taylor & Francis
We present an algorithm for calculating the conformational thermodynamics of large, flexible
molecules that combines ab initio electronic structure theory calculations with a torsional …
molecules that combines ab initio electronic structure theory calculations with a torsional …
CENCALC: A computational tool for conformational entropy calculations from molecular simulations
We present the CENCALC software that has been designed to estimate the conformational
entropy of single molecules from extended Molecular Dynamics (MD) simulations in the gas …
entropy of single molecules from extended Molecular Dynamics (MD) simulations in the gas …