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A multi-tree approach to compute transition paths on energy landscapes

Devaurs, Didier and Vaisset, Marc and Siméon, Thierry and Cortés, Juan A multi-tree approach to compute transition paths on energy landscapes. (2013) In: Workshop on Artificial Intelligence and Robotics Methods in Computational Biology, AAAI ‘13, July, 2013, 14 July 2013 - 18 July 2013, Bellevue, Washington, USA (Bellevue, United States).

(Document in English)

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Official URL: http://www.aaai.org/Press/Proceedings/aaai13.php


Exploring the conformational energy landscape of a molecule is an important but challenging problem because of the inherent complexity of this landscape. As part of this theme, various methods have been developed to compute transition paths between stable states of a molecule. Besides the methods classically used in biophysics/biochemistry, a recent approach originating from the robotics community has proven to be an efficient tool for conformational exploration. This approach, called the Transition-based RRT (T-RRT) is based on the combination of an effective path planning algorithm (RRT) with a Monte-Carlo-like transition test. In this paper, we propose an extension to T-RRT based on a multi-tree approach, which we call Multi-T-RRT. It builds several trees rooted at different interesting points of the energy landscape and allows to quickly gain knowledge about possible conformational transition paths. We demonstrate this on the alanine dipeptide.

Item Type:Conference or Workshop Item (Paper)
Audience (conference):International conference proceedings
Uncontrolled Keywords:
Institution:French research institutions > Centre National de la Recherche Scientifique - CNRS (FRANCE)
Université de Toulouse > Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
Université de Toulouse > Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE)
Université de Toulouse > Institut Supérieur de l'Aéronautique et de l'Espace - ISAE-SUPAERO (FRANCE)
Université de Toulouse > Université Toulouse III - Paul Sabatier - UT3 (FRANCE)
Université de Toulouse > Université Toulouse - Jean Jaurès - UT2J (FRANCE)
Laboratory name:
Deposited On:25 Jul 2013 09:19

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