The application of molecular fingerprints has a long history in computational medicinal chemistry, on the other side, gene microarray is playing an important role in bio-marker identification. Traditionally, these two technologies belong to different areas, i.e., chemoinformatics and bioinformatics, respectively. And they have never been jointly applied in one study yet. Recently, the appearance of small-molecular microarray data makes it possible to jointly use the compound structure information as well as gene-expression profile as a comprehensive description for drug study. Therefore, a novel approach is reported to describe compounds by integrating data from both of the two types, on the basis of the philosophy of the mutual complement of “essence” and “extension”. Comparing of the similarity searching results derived from the compound description with only the structure fingerprint or the gene-expression profile, our integrated methodology indicated much better description ability. As a conclusion, our complementary description of chemical compound from an integration view of structure fingerprint and gene expression file will shed new light on the drug study in both area of bioinformatics and chemoinformatics. It is expected to provide more effective drug screening model with its great description ability and accelerate the process of drug design eventually.

Key words: molecular fingerprint, gene expression, small-molecular microarray, drug screening, complementary theory