What Can Human-Guided Simulations Bring to RNA Folding?

TitleWhat Can Human-Guided Simulations Bring to RNA Folding?
Publication TypeJournal Article
Year of Publication2017
AuthorsMazzanti L, Doutreligne S, Gageat C, Derreumaux P, Taly A, Baaden M, Pasquali S
JournalBiophys J
Volume113
Issue2
Pagination302-312
Date Published2017 Jul 25
ISSN1542-0086
KeywordsAccess to Information, Computer Simulation, Feedback, Psychological, Humans, Internet, Models, Genetic, Models, Molecular, RNA, RNA Folding, Software, Solvents
Abstract

Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures. Their structures and full trajectories have been analyzed statistically and compared to standard replica exchange molecular dynamics simulations. Our analyses show that participants gain easily chemical intelligence to fold simple and nontrivial topologies, with little computer time, and this result opens the door for the use of human-guided simulations to RNA folding. Our experiment shows that interactive simulations have better chances of success when the user widely explores the conformational space. Interestingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimental structure did not improve the quality of the proposed models.

DOI10.1016/j.bpj.2017.05.047
Alternate JournalBiophys. J.
Citation Key2017|2042
PubMed ID28648754
PubMed Central IDPMC5529179