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What Can Human-Guided Simulations Bring to RNA Folding?
Mazzanti, Liuba; Doutreligne, Sébastien; Gageat, Cedric; Derreumaux, Philippe; Taly, Antoine; Baaden, Marc; Pasquali, Samuela.
Afiliação
  • Mazzanti L; Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
  • Doutreligne S; Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
  • Gageat C; Département de Chimie, Ecole Normale Supérieure, PSL Research University, Université Pierre et Marie Curie, Sorbonne Paris Cité, Paris, France.
  • Derreumaux P; Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
  • Taly A; Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
  • Baaden M; Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
  • Pasquali S; Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France. Electronic address: samuela.pasquali@parisdescartes.fr.
Biophys J ; 113(2): 302-312, 2017 Jul 25.
Article em En | MEDLINE | ID: mdl-28648754
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.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Simulação por Computador / RNA / Dobramento de RNA Idioma: En Ano de publicação: 2017 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Simulação por Computador / RNA / Dobramento de RNA Idioma: En Ano de publicação: 2017 Tipo de documento: Article