In order to rank generated molecules, we proposed a new scoring type called candidate score to combine the results from QSAR and molecular docking experiments. The candidate score was calculated as the sum of z-scores of the predicted pIC 50 and the negative binding affinity values of the generated molecules. Then, the resulted compounds were ranked by the candidate score, in which molecules with higher candidate scores implied better potential on inhibiting VEGFR-2. Top ranked molecules were selected for further analysis.