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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment

Abstract

The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template group). For most of the targets, the contact restraints were derived from the server models top-ranked by the DeepQA method, while the DNCON2 method was used for 11 targets. Our consensus- fragment procedure was used to run template-assisted predictions. Each group also processed the Nuclear Magnetic Resonance (NMR)- and Small Angle X-Ray Scattering (SAXS)-data assisted targets. The average Global Distance Test Total Score (GDT TS) of the ‘Model 1’ predictions were 29.17, 39.32, and 56.37 for the UNRES, UNRES-contact, and UNRES-template predictions, respectively, increasing by 0.53, 2.24, and 3.76, respectively, compared to CASP13. It was also found that the GDT TS of the UNRES models obtained in ab initio mode and in the contact-assisted mode decreases with the square root of chain length, while the exponent in this relationship is 0.20 for the UNRES-template group models and 0.11 for the best performing AlphaFold2 models, which suggests that incorporation of database information, which stems from protein evolution, brings in long-range correlations, thus enabling the correction of force-field inaccuracies.

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DOI:
Digital Object Identifier (open in new tab) 10.1016/j.jmgm.2021.108008
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Category:
Articles
Type:
artykuły w czasopismach
Published in:
JOURNAL OF MOLECULAR GRAPHICS & MODELLING no. 108,
ISSN: 1093-3263
Language:
English
Publication year:
2021
Bibliographic description:
Antoniak A., Biskupek I., Bojarski K. K., Czaplewski C., Giełdoń A., Kogut M., Kogut M. M., Krupa P., Lipska A., Liwo A., Lubecka E., Marcisz M., Maszota-Zieleniak M., Samsonov S. A., Sieradzan A. K., Ślusarz M. J., Ślusarz R., Wesołowski P. A., Ziȩba K.: Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment// JOURNAL OF MOLECULAR GRAPHICS & MODELLING -Vol. 108, (2021), s.108008-
DOI:
Digital Object Identifier (open in new tab) 10.1016/j.jmgm.2021.108008
Verified by:
Gdańsk University of Technology

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