Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets

Agnieszka Karczyńska , Magdalena Mozolewska , Paweł Krupa , Artur Giełdoń , Krzysztof Bojarski , Bartłomiej Zaborowski , Józef Adam Liwo , Rafał Ślusarz , Magdalena Ślusarz , Jooyoung Lee , Keehyoung Joo , Cezary Czaplewski

Abstract

Knowledge-based methods are, at present, the most effective ones for the prediction of protein structures; however, their results heavily depend on the similarity of a target sequence to those of proteins with known structures. On the other hand, the physics-based methods, although still less accurate and more expensive to execute, are independent of databases and give reasonable results where the knowledge-based methods fail because of weak sequence similarity. Therefore, a plausible approach seems to be the use of knowledge-based methods to determine the sections of the structures that correspond to sufficient sequence similarity and physics-based methods to determine the remaining structure. By participating in the 12th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP12) as the KIAS-Gdansk group, we tested our recently developed hybrid approach, in which protein-structure prediction is carried out by using the physicsbased UNRES coarse-grained energy function, with restraints derived from the server models. Best predictions among all groups were obtained for 2 targets and 80% of our models were in the upper 50% of the models submitted to CASP. Our method was also able to exclude, with about 70% confidence, the information from the servers that performed poorly on a given target. Moreover, the method resulted in the best models of 2 refinement targets and performed remarkably well on oligomeric targets.
Author Agnieszka Karczyńska (FCh / DTCh / LMM)
Agnieszka Karczyńska,,
- Laboratory of Molecular Modeling
, Magdalena Mozolewska (FCh / DTCh / LMM) - [Polish Academy of Science]
Magdalena Mozolewska,,
- Laboratory of Molecular Modeling
- Polska Akademia Nauk
, Paweł Krupa (FCh / DTCh / LSP) - [Polish Academy of Science]
Paweł Krupa,,
- Laboratory of Simulation of Polymers
- Polska Akademia Nauk
, Artur Giełdoń (FCh / DTCh / LSP)
Artur Giełdoń,,
- Laboratory of Simulation of Polymers
, Krzysztof Bojarski (FCh / DTCh / LMM)
Krzysztof Bojarski ,,
- Laboratory of Molecular Modeling
, Bartłomiej Zaborowski (FCh / DTCh / LSP)
Bartłomiej Zaborowski,,
- Laboratory of Simulation of Polymers
, Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
, Rafał Ślusarz (FCh / DOCh / LCCh)
Rafał Ślusarz,,
- Laboratory of Carbohydrate Chemistry
, Magdalena Ślusarz (FCh / DTCh / LMM)
Magdalena Ślusarz,,
- Laboratory of Molecular Modeling
, Jooyoung Lee
Jooyoung Lee,,
-
et al.`
Journal seriesJournal of Molecular Graphics & Modelling, ISSN 1093-3263, (A 25 pkt)
Issue year2018
Vol83
Pages92-99
Publication size in sheets0.5
Keywords in Englishprotein structure prediction, UNRES force field, knowledge-based methods, template-based restraints, replica exchange molecular dynamics
DOIDOI:10.1016/j.jmgm.2018.05.008
URL https://doi.org/10.1016/j.jmgm.2018.05.008
Languageen angielski
Score (nominal)25
ScoreMinisterial score = 25.0, 20-09-2018, ArticleFromJournal
Ministerial score (2013-2016) = 25.0, 20-09-2018, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 1.754 (2) - 2016=1.813 (5)
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