藥物設計剛開始最重要的就是先找到先導化合物。電腦輔助藥物設計方法能縮短先導化合物的發現。如果R＆D時間能縮短2∼3年，那麼不但能簡短R＆D的經費，而且增加上市的獲利時間，這將帶來很大的經濟效益及利潤。因而CADD方法已成為國外藥廠研發新藥的趨勢，並且有不少成功的例子，相信在電腦時代該技術將成為未來的主要潮流。本論文以直接藥物設計建立一組最適HLA-DR4的screening model並以間接藥物設計進行交互驗證。

免疫反應開始於MHC-binding peptide 間的鍵結強度超過某個門檻,不論這個binding peptide的來源是self-peptide or non self-peptide，我們可藉由MHC-binding peptide間鍵結的研究，發展傳染病疫苗的設計和對自我免疫反應疾病及cancer的immunotherapies。

本論文所建立最適HLA-DR4的screening model為”經由GOLD產生conformation後，再由GLIDE(Rigidly Docking)進行screening”。

藉由Ludi在活性部位設計出43個可能之抑制劑，分別以所建立screening model及catalyst進行預測並由chi-square independence test檢定出所建立之screening model預測結果與catalyst 預測結果確具相關性--交叉驗證，最後發現8較實驗更具抑制能力之抑制劑。

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