Skip Navigation

Bioinformatics 2007 23(13):i408-i417; doi:10.1093/bioinformatics/btm191
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Rossi, R.
Right arrow Articles by Redon, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rossi, R.
Right arrow Articles by Redon, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design

Romain Rossi 1, Mathieu Isorce 2, Sandy Morin 1, Julien Flocard 2, Karthik Arumugam 2, Serge Crouzy 2, Michel Vivaudou 3 and Stephane Redon 1,*

1i3D - INRIA Rhône-Alpes, 655 avenue de l'Europe, 38334 Saint-Ismier Cedex,2Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant, Université Joseph Fourier UMR 5249, CEA Grenoble, 17, rue des martyrs, 38054 Grenoble Cedex 9 and3Institut de Biologie Structurale, UMR5075 CEA-CNRS-Univ. J. Fourier 41, rue Jules Horowitz, 38027 Grenoble, France

*To whom correspondence should be addressed.


  Abstract

Motivation: The cost of molecular quasi-statics or dynamics simulations increases with the size of the simulated systems, which is a problem when studying biological phenomena that involve large molecules over long time scales. To address this problem, one has often to either increase the processing power (which might be expensive), or make arbitrary simplifications to the system (which might bias the study).

Results: We introduce adaptive torsion-angle quasi-statics, a general simulation method able to rigorously and automatically predict the most mobile regions in a simulated system, under user-defined precision or time constraints. By predicting and simulating only these most important regions, the adaptive method provides the user with complete control on the balance between precision and computational cost, without requiring him or her to perform a priori, arbitrary simplifications. We build on our previous research on adaptive articulated-body simulation and show how, by taking advantage of the partial rigidification of a molecule, we are able to propose novel data structures and algorithms for adaptive update of molecular forces and energies. This results in a globally adaptive molecular quasi-statics simulation method. We demonstrate our approach on several examples and show how adaptive quasi-statics allows a user to interactively design, modify and study potentially complex protein structures.

Contact: stephane.redon{at}inria.fr


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.