虛擬藥物篩選利用了Qsar以及Docking兩種方法來進行電腦模擬，要觀察藥物分子與蛋白質結合後的穩定結構就必須依靠Docking。從1980年左右開始研究至今，許多Docking的軟體相繼被研發出來，但由於這些軟體有著許多的缺點。目前常用的Docking軟體主要的缺點有：速度不夠快、剛性的蛋白質與活性化合物結構、準確率不佳、沒有考慮接合後的極化現象。導致虛擬藥物篩選目前仍然停留在輔助的角色。
並且虛擬藥物篩選在進行蛋白質與藥物對接都是直接使用蛋白質結晶結構來進行 Docking，並且針對 Docking 完成後蛋白質與藥物分子的接合分值來判斷蛋白質與藥物分子的作用。
本篇論文探討了蛋白質結構在人體環境中的構象變化與結晶結構的差異，以及在水溶液環境中構象改變的蛋白質對藥物分子進行 Docking 的能量分布是否與結晶結構的蛋白質對藥物分子進行 Docking 能量分布有所差異，並且在最後也探討了抗憂鬱症中藥分子以及西藥分子Docking上蛋白質後的作用情形以及移動情形，進而去推測中藥分子與西藥分子在抑制憂鬱症的機制上是否有所差異。

Docking and Qsar are two kinds of the methods in virtual screeing. Observing the stable structure of drug molecules and protein must rely on docking. Studies from around 1980 to now, many docking software have been developed. But these software have many short comings. The software currently used for docking have many disadvantage: poor efficiency, rigid structure of the proteins and the ligands, poor accuracy, without the polarization after binding, leading virtual screening is still stuck in a supporting role.
Virtual drug screeing are using the crystal structure of protein directly. And, after the docking, using the binding energy to determine the effect of protein and drug molecules.
This paper explores the protein structures in the human environment conformational change and differences structure between crystal protein and ours.
After the docking, Comparing the binding energy distribution between the crystal protein and ours. We also discuss the role of situation between western medicine molecules and traditional chinese medicine molecules when docking on protein Successfully. Finally, we try to speculate the reaction of the medicine molecules in the protein active sites.

誌 謝 i
摘 要 i
Abstract iii
目 錄 iii
圖 　次 vi
表 　次 viii
第一章 簡介 1
1.1 前言 1
1.2 Docking（對接）簡介 2
1.3 本次實驗所用蛋白質與活性化合物簡介 4
第二章 實驗方法 5
2.1 AMBER力場 5
2.2轉動慣量與慣性張量 6
2.3實驗的流程及細節 7
2.4模擬用蛋白質與活性化合物 15
第三章 結果與討論 28
3.1蛋白質在水溶液環境中的構象變化 28
3.2蛋白質與藥物對接後能量分布探討 32
3.3藥物蛋白質動力模擬探討 32
第四章 結論 42
參考文獻 43
附錄 45
附表一 45

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