Through various high-throughput experimental projects for analyzing the genome, transcriptome and proteome, we are beginning to understand the genomic spaces. Simultaneously, the high-throughput screening of large-scale chemical compound libraries with various biological assays enable us to explore the chemical space. However, our knowledge about the relationship between the chemical and genomic spaces is very limited. For example, the PubChem database at NCBI [1] stores information on millions of chemical compounds, but the number of compounds with information on their target protein is very limited [2]. Therefore, there is a strong incentive to develop new methods capable of detecting these potential target-ligand interactions efficiently.