結構基因體學和x-ray，NMR等實驗方法的快速發展，使得蛋白質的結構往往比其所屬功能可更快一步的得知.而對於這些已先有結構的蛋白質，為進一步知其所屬功能，必需佐以各種生化實驗。儘管這些生化實驗能夠提供極為準確的訊息，但所需耗費的人力，時間卻甚為可觀。因此，本論文的研究目標為發展電腦輔助的方法來有效偵測這些已先有結構的蛋白質之所屬功能。同時，有鑒於蛋白質與巨分子之間作用力對細胞的重要性，因此所研究的蛋白質將著重於與DNA/RNA/蛋白質這三種巨分子有作用力的類型上。於論文第一章中，我們將簡述以往的相關研究。
於論文第二章中，我們發現在蛋白質上這些巨分子結合位置均擁有一個共通的特徵，即是他們傾向位於擁有高靜電和高凡得瓦張力的區域。同時藉由進一步的分析，我們了解到，即使這些巨分子結合位置擁有高靜電和高凡得瓦張力的特徵，不同的巨分子結合位置其高靜電和高凡得瓦張力的程度表現上仍有顯著上的差異。並由此差異，我們可辨識出不同的巨分子結合位置。
於論文第三章中，我們發展預測方法來偵測 DNA-binding protein 結構上的 DNA 結合位置。此預測方法須利用 DNA-binding protein 結構上靜電和演化上的訊息。而在本章中我們發展的預測方法將與以往的預測方法進行一連串的比較，同時，此法成功的被運用於 DNA-free 的蛋白質結構狀態下。
於論文第四章中，我們發展預測方法來偵測 RNA-binding protein 結構上的 RNA 結合位置。此預測方法須利用 RNA-binding protein 結構上靜電、演化和構形等的訊息。我們並更進一步的將此法成功的運用於 RNA-free 的蛋白質結構狀態。
最後，於論文第五章中，對於先前的第二、三和四章節，我們提出整合性的結論，同時對於之後有興趣的主題加以簡述。

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