Maximum likelihood calibration of the UNRES force field for simulation of protein structure and dynamics

Paweł Krupa , Anna Hałabis , Wioletta Żmudzińska , Stanisław Ołdziej , H. A. Scheraga , Józef Adam Liwo

Abstract

By using the maximum likelihood method for force-field calibration recently developed in our laboratory, which is aimed at achieving the agreement between the simulated conformational ensembles of selected training proteins and the corresponding ensembles determined experimentally at various temperatures, the physics-based coarse-grained UNRES force field for simulations of protein structure and dynamics was optimized with seven small training proteins exhibiting a variety of secondary and tertiary structures. Four runs of optimization, in which the number of optimized force-field parameters was gradually increased, were carried out, and the resulting force fields were subsequently tested with a set of 22 α-, 12 β-, and 12 α + β-proteins not used in optimization. The variant in which energy-term weights, local, and correlation potentials, side-chain radii, and anisotropies were optimized turned out to be the most transferable and outperformed all previous versions of UNRES on the test set.
Author Paweł Krupa PSP - [Polish Academy of Science]
Paweł Krupa,,
- Laboratory of Simulation of Polymers
- Polska Akademia Nauk
, Anna Hałabis MWB UG i GUMed
Anna Hałabis,,
- Intercollegiate Faculty of Biotechnology UG
, Wioletta Żmudzińska PSB
Wioletta Żmudzińska,,
- Laboratory of Biopolymers Structure
, Stanisław Ołdziej PSB
Stanisław Ołdziej,,
- Laboratory of Biopolymers Structure
, H. A. Scheraga
H. A. Scheraga,,
-
, Józef Adam Liwo PMM
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
Journal seriesJournal of Chemical Information and Modeling, ISSN 1549-9596
Issue year2017
Vol57
No9
Pages2364-2377
Publication size in sheets0.65
DOIDOI:10.1021/acs.jcim.7b00254
URL http://pubs.acs.org/doi/pdf/10.1021/acs.jcim.7b00254
Languageen angielski
Score (nominal)40
ScoreMinisterial score = 40.0, 20-12-2017, ArticleFromJournal
Ministerial score (2013-2016) = 40.0, 20-12-2017, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 3.76 (2) - 2016=4.066 (5)
Citation count*6 (2018-06-23)
Cite
Share Share



* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
Back