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This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Bioinformatics

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An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds

Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato and Yasubumi Sakakibara*

Author affiliations

Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan

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Citation and License

BMC Bioinformatics 2012, 13(Suppl 17):S8  doi:10.1186/1471-2105-13-S17-S8

Published: 13 December 2012



Prediction of biochemical (metabolic) pathways has a wide range of applications, including the optimization of drug candidates, and the elucidation of toxicity mechanisms. Recently, several methods have been developed for pathway prediction to derive a goal compound from a start compound. However, these methods require high computational costs, and cannot perform comprehensive prediction of novel metabolic pathways. Our aim of this study is to develop a de novo prediction method for reconstructions of metabolic pathways and predictions of unknown biosynthetic pathways in the sense that it does not require any initial network such as KEGG metabolic network to be explored.


We formulated pathway prediction between a start compound and a goal compound as the shortest path search problem in terms of the number of enzyme reactions applied. We propose an efficient search method based on A* algorithm and heuristic techniques utilizing Linear Programming (LP) solution for estimation of the distance to the goal. First, a chemical compound is represented by a feature vector which counts frequencies of substructure occurrences in the structural formula. Second, an enzyme reaction is represented as an operator vector by detecting the structural changes to compounds before and after the reaction. By defining compound vectors as nodes and operator vectors as edges, prediction of the reaction pathway is reduced to the shortest path search problem in the vector space. In experiments on the DDT degradation pathway, we verify that the shortest paths predicted by our method are biologically correct pathways registered in the KEGG database. The results also demonstrate that the LP heuristics can achieve significant reduction in computation time. Furthermore, we apply our method to a secondary metabolite pathway of plant origin, and successfully find a novel biochemical pathway which cannot be predicted by the existing method. For the reconstruction of a known biochemical pathway, our method is over 40 times as fast as the existing method.


Our method enables fast and accurate de novo pathway predictions and novel pathway detection.