The general theory of the construction of scale-consistent energy terms in the coarse-grained force fields presented in Paper I of this series has been applied to the revision of the UNRES force field for physics-based simulations of proteins. The potentials of mean force corresponding to backbone-local and backbone-correlation energy terms were calculated from the ab initio energy surfaces of terminally blocked glycine, alanine, and proline, and the respective analytical expressions, derived by using the scale-consistent formalism, were fitted to them. The parameters of all these potentials depend on single-residue types, thus reducing their number and preventing over-fitting. The UNRES force field with the revised backbone-local and backbone-correlation terms was calibrated with a set of four small proteins with basic folds: tryptophan cage variant (TRP1; α), Full Sequence Design (FSD; α + β), villin headpiece (villin; α), and a truncated FBP-28 WW-domain variant (2MWD; β) (the NEWCT-4P force field) and, subsequently, with an enhanced set of 9 proteins composed of TRP1, FSD, villin, 1BDC (α), 2I18 (α), 1QHK (α + β), 2N9L (α + β), 1E0L (β), and 2LX7 (β) (the NEWCT-9P force field). The NEWCT-9P force field performed better than NEWCT-4P in a blind-prediction-like test with a set of 26 proteins not used in calibration and outperformed, in a test with 76 proteins, the most advanced OPT-WTFSA-2 version of UNRES with former backbone-local and backbone-correlation terms that contained more energy terms and more optimizable parameters. The NEWCT-9P force field reproduced the bimodal distribution of backbone-virtual-bond angles in the simulated structures, as observed in experimental protein structures.
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21 April 2019
Research Article|
April 18 2019
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation
Adam Liwo
;
Adam Liwo
a)
1
Faculty of Chemistry, University of Gdańsk
, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
2
School of Computational Sciences, Korea Institute for Advanced Study
, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
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Adam K. Sieradzan;
Adam K. Sieradzan
1
Faculty of Chemistry, University of Gdańsk
, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
2
School of Computational Sciences, Korea Institute for Advanced Study
, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
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Agnieszka G. Lipska
;
Agnieszka G. Lipska
1
Faculty of Chemistry, University of Gdańsk
, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
2
School of Computational Sciences, Korea Institute for Advanced Study
, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
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Cezary Czaplewski;
Cezary Czaplewski
1
Faculty of Chemistry, University of Gdańsk
, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
2
School of Computational Sciences, Korea Institute for Advanced Study
, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
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InSuk Joung;
InSuk Joung
2
School of Computational Sciences, Korea Institute for Advanced Study
, 87 Hoegiro, Dongdaemun-gu, 130-722 Seoul, South Korea
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Wioletta Żmudzińska;
Wioletta Żmudzińska
3
Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk
, ul. Abrahama 58, 80-307 Gdańsk, Poland
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Anna Hałabis;
Anna Hałabis
3
Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk
, ul. Abrahama 58, 80-307 Gdańsk, Poland
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Stanisław Ołdziej
Stanisław Ołdziej
3
Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk
, ul. Abrahama 58, 80-307 Gdańsk, Poland
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J. Chem. Phys. 150, 155104 (2019)
Article history
Received:
February 16 2019
Accepted:
March 28 2019
Citation
Adam Liwo, Adam K. Sieradzan, Agnieszka G. Lipska, Cezary Czaplewski, InSuk Joung, Wioletta Żmudzińska, Anna Hałabis, Stanisław Ołdziej; A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. J. Chem. Phys. 21 April 2019; 150 (15): 155104. https://doi.org/10.1063/1.5093015
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