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Nucleic Acids Research 2005 33(Web Server Issue):W605-W610; doi:10.1093/nar/gki447
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

A. Xayaphoummine1, T. Bucher1 and H. Isambert1,2,*

1Laboratoire de Dynamique des Fluides Complexes, CNRS-ULP, Institut de Physique 3 rue de l'Université, 67000 Strasbourg, France 2Physico-chimie Curie, CNRS UMR168, Institut Curie, Section de Recherche 11 rue P. & M. Curie, 75005 Paris, France

*To whom correspondence should be addressed. Tel: +33 1 42 34 64 74; Email: herve.isambert{at}curie.fr

Received February 15, 2005. Revised March 31, 2005. Accepted March 31, 2005.

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at http://kinefold.curie.fr/.


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