Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing

Adam Sieradzan , Łukasz Golon , Józef Adam Liwo


A physics-based method for the prediction of the structures of nucleic acids, which is based on the physics-based 2-bead NARES-2P model of polynucleotides and global-optimization Conformational Space Annealing (CSA) algorithm has been proposed. The target structure is sought as the global-energy-minimum structure, which ignores the entropy component of the free energy but spares expensive multicanonical simulations necessary to find the conformational ensemble with the lowest free energy. The CSA algorithm has been modified to optimize its performance when treating both single and multi-chain nucleic acids. It was shown that the method finds the native fold for simple RNA molecules and DNA duplexes and with limited distance restraints, which can easily be obtained from the secondary-structure-prediction servers, complex RNA folds can be treated with using moderate computer resources.
Author Adam Sieradzan (FCh/DTCh/LMM)
Adam Sieradzan,,
- Laboratory of Molecular Modeling
, Łukasz Golon (FCh/DTCh/LMM)
Łukasz Golon,,
- Laboratory of Molecular Modeling
, Józef Adam Liwo (FCh/DTCh/LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
Journal seriesPhysical Chemistry Chemical Physics, ISSN 1463-9076, e-ISSN 1463-9084, (A 40 pkt)
Issue year2018
Publication size in sheets0.50
Keywords in Englishsecondary structure prediction; nucleic-acids; selenium derivatization; global optimization; molecular-structure; protein-structure; 3d structure; model; puzzles; crystallography
ASJC Classification1606 Physical and Theoretical Chemistry; 3100 General Physics and Astronomy
Languageen angielski
Score (nominal)40
Score sourcejournalList
ScoreMinisterial score = 40.0, 28-01-2020, ArticleFromJournal
Publication indicators WoS Citations = 0.000; Scopus SNIP (Source Normalised Impact per Paper): 2016 = 1.117; WoS Impact Factor: 2018 = 3.567 (2) - 2018=3.963 (5)
Citation count*1 (2020-06-25)
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