Metabolism defines a series of chemical reactions that occur in a cell, maintaining the lives of living organisms by supplying the necessary molecules and energy 
. Metabolism is composed of metabolic pathways in which chemical reactions are organized in such a way that one molecule is transformed into another through a cascade of reactions recruiting small molecules and enzymes. Thus, small molecules and enzymes are part of the basic components of metabolic pathways. Determining the functioning of the small molecules and enzymes of each metabolic pathway is key to understanding the metabolic pathway and its biological functions.
During the past decade, large amounts of information concerning different organisms have been gathered on both the genetic and metabolic levels. Some databases pertaining to chemicals and proteins, such as KEGG (Kyoto Encyclopedia of Genes and Genomes) 
, ENZYME 
, STITCH (Search Tool for Interactions of Chemicals) 
and STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) 
, have been established, from which descriptions of the properties of small molecules and enzymes can be readily acquired. Such information also provides an opportunity to study the metabolic pathways in greater detail computationally. A computational approach is another avenue by which to gain insight into metabolic pathways, apart from biochemical experiments. In recent years, some efforts 
have been made to tackle the problem by mapping small molecules to the corresponding metabolic pathways. However, besides small molecules, enzymes are also important basic components of metabolic pathways. As far as we know, this study is the first to map small molecules and enzymes to the metabolic pathways simultaneously, thus providing some additional information for use in studying metabolic pathways.
A large body of data concerning protein-protein interactions and chemical-chemical interactions has been applied extensively to predicting the attributes of proteins and compounds 
. This work led to the conclusion that interactive proteins or interactive compounds were more likely to share common biological functions than non-interactive ones. Most of these approaches studied chemical-chemical interactions or protein-protein interactions separately to construct classification models. In this study, we proposed a novel method, integrating interactions among chemicals and proteins including chemical-chemical interactions, protein-protein interactions, and chemical-protein interactions, to predict metabolic pathways in which small molecules and enzymes of yeast participate. Since some small molecules and enzymes participate in more than one metabolic pathway, our method sorts the probabilities of metabolic pathways to which a small molecule or enzyme may belong rather than predicting only the most probable metabolic pathway.