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

Abstrakt

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:
Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1016/j.jmgm.2021.108008
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Creative Commons: CC-BY-NC-ND otwiera się w nowej karcie

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Kategoria:
Publikacja w czasopiśmie
Typ:
artykuły w czasopismach
Opublikowano w:
JOURNAL OF MOLECULAR GRAPHICS & MODELLING nr 108,
ISSN: 1093-3263
Język:
angielski
Rok wydania:
2021
Opis bibliograficzny:
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:
Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1016/j.jmgm.2021.108008
Weryfikacja:
Politechnika Gdańska

wyświetlono 165 razy

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