Randomized tree construction algorithm to explore energy landscapes

✍ Scribed by Léonard Jaillet; Francesc J. Corcho; Juan-Jesús Pérez; Juan Cortés

• Book ID: 102306182
• Publisher: John Wiley and Sons
• Year: 2011
• Tongue: English
• Weight: 462 KB
• Volume: 32
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.21931

✦ Synopsis

Abstract

In this work, a new method for exploring conformational energy landscapes is described. The method, called transition‐rapidly exploring random tree (T‐RRT), combines ideas from statistical physics and robot path planning algorithms. A search tree is constructed on the conformational space starting from a given state. The tree expansion is driven by a double strategy: on the one hand, it is naturally biased toward yet unexplored regions of the space; on the other, a Monte Carlo‐like transition test guides the expansion toward energetically favorable regions. The balance between these two strategies is automatically achieved due to a self‐tuning mechanism. The method is able to efficiently find both energy minima and transition paths between them. As a proof of concept, the method is applied to two academic benchmarks and the alanine dipeptide. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011