Concept

Conformational entropy

Related publications (33)

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy

Sebastian James Davis

Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native conformation of glob ...

NATL ACAD SCIENCES2022

Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure

Diana Kornelia Morzy, Himanshu Joshi

DNA nanotechnology has emerged as a promising method for designing spontaneously inserting and fully controllable synthetic ion channels. However, both insertion efficiency and stability of existing DNA-based membrane channels leave much room for improveme ...

AMER CHEMICAL SOC2021

Hamiltonian-Reservoir Replica Exchange and Machine Learning Potentials for Computational Organic Chemistry

Alberto Fabrizio, Benjamin André René Meyer, Raimon Fabregat I De Aguilar-Amat, Daniel Hollas

This work combines a machine learning potential energy function with a modular enhanced sampling scheme to obtain statistically converged thermodynamical properties of flexible medium-size organic molecules at high ab initio level. We offer a modular envir ...

AMER CHEMICAL SOC2020

Entropy as a tool for crystal discovery

Pablo Miguel Piaggi

The computational prediction of crystal structures has emerged as an useful alternative to expensive and often cumbersome experiments. We propose an approach to the prediction of crystal structures and polymorphism based on reproducing the crystallization ...

EPFL2019

Entropy production for coarse-grained dynamics

Daniel Maria Busiello, Amos Maritan

Systems out of equilibrium exhibit a net production of entropy. We study the dynamics of a stochastic system represented by a Master equation (ME) that can be modeled by a Fokker-Planck equation in a coarse-grained, mesoscopic description. We show that the ...

2019

Predicting polymorphism in molecular crystals using orientational entropy

Pablo Miguel Piaggi, Michele Parrinello

We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This id ...

2018

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

Kai Johnsson, Alberto Schena

Attempts to create novel ligand-binding proteins often focus on formation of a binding pocket with shape complementarity against the desired ligand (particularly for compounds that lack distinct polar moieties). Although designed proteins often exhibit bin ...

OXFORD UNIV PRESS2018

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Bruno Emanuel Ferreira De Sousa Correia, Stefano Zamuner

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016

Molecular Level Characterization of the Structure and Interactions in Peptide-Functionalized Metal-Organic Frameworks

David Lyndon Emsley, Pierrick Berruyer

We use density functional theory, newly parameterized molecular dynamics simulations, and last generation N-15 dynamic nuclear polarization surface enhanced solid-state NMR spectroscopy (DNP SENS) to understand graft-host interactions and effects imposed b ...

2016

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