為了瞭解核酸-蛋白質複合物(Nucleic Acid-protein Complex)的功能需要詳細的三維結構資訊和胺基酸與其作用物之間的特性。在本論文中，我們開發一個用來辨識並以圖表方式輸出DNA與胺基酸之間作用的工具：iNucProt、歸納DNA中鹼基(Base)、五碳糖(Sugar)與磷酸根(Phosphate)和胺基酸之間作用的資料庫：dNucProt和用於預測蛋白質與DNA之間作用狀況的工具：pNucProt。iNucProt伺服器可讓使用者上傳蛋白質-DNA複合物的PDB檔案，分析辨識出檔案內作用的資訊後，以圖和表的方式輸出這些作用。這些分析結果整理出蛋白質與DNA的作用，包括與鹼基、五碳糖和磷酸根骨架發生的氫鍵(Hydrogen Bond)、透過水或金屬發生的作用(Water- or Metal-mediated Contact)、凡得瓦力(van der Waals contact)和疏水性作用(Hydrophobic Interaction)。iNucProt並提供的概要式的作用圖表示蛋白質與DNA之間的作用。dNucProt是利用iNucProt分析978個PDB檔案得來的。根據結果顯示，凡得瓦力、氫鍵、透過水發生的氫鍵、透過金屬發生的氫鍵和疏水性作用在DNA與蛋白質之間的作用總數分別佔全部的68.59 %、21.03 %、7.11 %、2.85 %和0.42 %。胺基酸R和胺基酸K較偏好藉由凡得瓦力、氫鍵和透過水發生的氫鍵和鹼基G發生作用。相對地，我們辨識出胺基酸(胺基酸A、胺基酸T、胺基酸V和胺基酸K)較偏好藉由疏水性作用與鹼基(鹼基T和鹼基C)發生作用。pNucProt伺服器提供使用者上傳蛋白質-DNA複合物的蛋白質序列，利用iNucProt分析具有同源性(Homologous)蛋白質的三維結構後的結果和dNucProt，預測此蛋白質序列與DNA之間的作用。iNucProt、dNucProt和pNucProt都是用來幫助瞭解DNA與蛋白質之間作用的工具，其網頁位置在http://www.ncku-nucprot.idv.tw/。

Understanding the function of the nucleic acid-protein complex requires a detailed picture of 3D structure and the identity of crucial amino acid residues involved in its interactions with its targets. In this study, we developed iNucProt, a tool to identify and plot the interactions between DNA and protein, dNucProt, a database that summarized the interactions between the base, sugar, and phosphate of DNA and amino acids, and pNucProt, a tool to predict the interactions between DNA and protein. The iNucProt server enables users to submit the 3D coordinates of the protein-DNA complex from a PDB file, and then it identifies the interactions using schematic diagrams and tables. It provides a summary description of protein-DNA interactions, including hydrogen bonds, water- or metal-mediated contacts, van der Waals contacts, and hydrophobic interactions, from bases, phosphate backbones, and sugars. It also generates schematic diagrams representing DNA-binding interactions. The dNucProt database was built from the analysis of 978 PDB entries using iNucProt. The results showed that van der Waals contacts, hydrogen bonds, water-mediated hydrogen bonds, metal-mediated contacts, and hydrophobic interactions between DNA and protein were 68.59 %, 21.03 %, 7.11 %, 2.85 %, and 0.42 %, respectively. Arginine and lysine prefer to interact with guanine via van der Waals contacts, hydrogen bonds, and water-mediated hydrogen bonds. In contrast, hydrophobic interactions between amino acids (alanine, tyosine, valine, and lysine) and the bases (thymine and cytosine) were identified. The pNucProt server enables users to submit the amino acid sequence of DNA-binding protein, and then it predicts its DNA interactions using the results of 3D structures of homologous proteins analyzed by iNucProt and the dNucProt database. iNucProt, dNucProt, and pNucProt are ccomprehensive tools for understanding the interactions between DNA and protein and are available at http://www.ncku-nucprot.idv.tw/.

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