Journal
ARTIFICIAL INTELLIGENCE IN MEDICINE
Volume 39, Issue 1, Pages 49-63Publisher
ELSEVIER
DOI: 10.1016/j.artmed.2006.04.004
Keywords
protein folding; estimation of distribution algorithms; protein structure prediction; rotamers
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Objective: This paper presents an algorithm for the solution of the side chain placement problem. Methods and materials: The algorithm combines the application of the Goldstein elimination criterion with the univariate marginal distribution algorithm (UMDA), which stochastically searches the space of possible solutions. The suitability of the algorithm to address the problem is investigated using a set of 425 proteins. Results: For a number of difficult instances where inference algorithms do not converge, it has been shown that UMDA is able to find better structures. Conclusions: The results obtained show that the algorithm can achieve better structures than those obtained with other state-of-the-art methods like inference-based techniques. Additionally, a theoretical and empirical analysis of the computationat cost of the algorithm introduced has been presented. (C) 2006 Elsevier B.V. All rights reserved.
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