Protein-ligand interaction energy-based entropy calculations: fundamental challenges for flexible systems
Gergely Kohut , Józef Adam Liwo , Szilvia Bösze , Tamás Beke-Somfai , Sergey Samsonov
AbstractEntropy calculations represent one of the most challenging steps in obtaining the binding free energy in biomolecular systems. A novel computationally effective approach (IE) was recently proposed to calculate the entropy based on the computation of protein-ligand interaction energy directly from molecular dynamics (MD) simulations. We present a study focused on the application of this method to flexible molecular systems and compare its performance with well-established normal mode (NM) and quasiharmonic (QH) entropy calculation approaches. Our results demonstrated that the IE method is intended for calculating entropy change for binding partners in fixed conformations, as by the original definition of IE, and is not applicable to the molecular complexes in which the interacting partners undergo significant conformational changes during the binding process.
|Journal series||Journal of Physical Chemistry B, ISSN 1520-6106, (A 30 pkt)|
|Publication size in sheets||0.5|
|Score|| = 30.0, 31-08-2018, ArticleFromJournal|
= 30.0, 31-08-2018, ArticleFromJournal
|Publication indicators||: 2016 = 3.177 (2) - 2016=3.177 (5)|
|Citation count*||2 (2019-01-18)|
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.