Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment

Emilia A Lubecka; Agnieszka S Karczyńska; Agnieszka G Lipska; Adam K Sieradzan; Karolina Ziȩba; Celina Sikorska; Urszula Uciechowska; Sergey A Samsonov; Paweł Krupa; Magdalena A Mozolewska; Łukasz Golon; Artur Giełdoń; Cezary Czaplewski; Rafał Ślusarz; Magdalena Ślusarz; Silvia N Crivelli; Adam Liwo

doi:10.1016/j.jmgm.2019.07.013

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment

J Mol Graph Model. 2019 Nov:92:154-166. doi: 10.1016/j.jmgm.2019.07.013. Epub 2019 Jul 26.

Authors

Emilia A Lubecka¹, Agnieszka S Karczyńska², Agnieszka G Lipska², Adam K Sieradzan², Karolina Ziȩba², Celina Sikorska², Urszula Uciechowska², Sergey A Samsonov², Paweł Krupa³, Magdalena A Mozolewska⁴, Łukasz Golon², Artur Giełdoń², Cezary Czaplewski², Rafał Ślusarz², Magdalena Ślusarz², Silvia N Crivelli⁵, Adam Liwo⁶

Affiliations

¹ Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Wita Stwosza 57, 80-308, Gdańsk, Poland; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
² Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
³ Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw, PL, 02668, Poland.
⁴ Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warsaw, 01-248, Poland.
⁵ Department of Computer Science, UC Davis, One Shields Ave., Davis, CA, 95616, USA.
⁶ Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, 130-722, Seoul, Republic of Korea. Electronic address: adam.liwo@ug.edu.pl.

PMID: 31376733
DOI: 10.1016/j.jmgm.2019.07.013

Abstract

The recent NEWCT-9P version of the coarse-grained UNRES force field for proteins, with scale-consistent formulas for the local and correlation terms, has been tested in the CASP13 experiment of the blind-prediction of protein structure, in the ab initio, contact-assisted, and data-assisted modes. Significant improvement of the performance has been observed with respect to the CASP11 and CASP12 experiments (by over 10 GDT_TS units for the ab initio mode predictions and by over 15 GDT_TS units for the contact-assisted prediction, respectively), which is a result of introducing scale-consistent terms and improved handling of contact-distance restraints. As in previous CASP exercises, UNRES ranked higher in the free modeling category than in the general category that included template based modeling targets. Use of distance restraints from the predicted contacts, albeit many of them were wrong, resulted in the increase of GDT_TS by over 8 units on average and introducing sparse restraints from small-angle X-ray/neutron scattering and chemical cross-link-mass-spectrometry experiments, and ambiguous restraints from nuclear magnetic resonance experiments has also improved the predictions by 8.6, 9.7, and 10.7 GDT_TS units on average, respectively.

Keywords: Free and data-assisted modeling; Multiscale modeling; Replica-exchange molecular dynamics; UNRES force field; protein structure prediction.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Golgi Matrix Proteins / chemistry
Models, Molecular*
Peptides / chemistry
Protein Conformation*
Proteins / chemistry*

Substances

Golgi Matrix Proteins
Peptides
Proteins