The final, formatted version of the article will be published soon.
MINI REVIEW article
Front. Phys.
Sec. Biophysics
Volume 12 - 2024 |
doi: 10.3389/fphy.2024.1469515
This article is part of the Research Topic Atomistic Simulations of Biological and Nanostructured Materials for Practical Applications View all articles
Free Energy Calculations in Biomolecule-Nanomaterial Interactions
Provisionally accepted- Zhejiang University of Science and Technology, Hangzhou, China
In computational chemistry and molecular modeling, the interactions between biomolecules (BMs) and nanomaterials (NMs) play a crucial role in various physical and biological processes, and have significant implications in material discovery and development. While there is extensive literature on free energy calculations for drugtarget interactions, reviews specifically addressing BM-NM interactions are relatively scarce. This manuscript aims to fill in this gap by presenting a comprehensive overview of the most widely used and well-established methods for free energy calculations. It provides a detailed analysis of the advantages and limitations of these methods and discusses their applicability to BM-NM systems. This work is intended to offer insights into free energy calculations and serve as a guide for future research in this field.
Keywords: MM/PBSA, Free Energy Perturbation (FEP), thermodynamic integration, Bennett acceptance ratio (BAR), Umbrella sampling (US), Jarzynski equality, Metadynamics, Free energy calculations
Received: 24 Jul 2024; Accepted: 03 Sep 2024.
Copyright: © 2024 Fu, Zhu and CHEN. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
QU CHEN, Zhejiang University of Science and Technology, Hangzhou, China
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.