Pine-MD (Protein INformation Extraction from Molecular Dynamics Simulation) 是一套由本實驗室自行發展，運作於Linux指令模式下，用來進行分析分子動態模擬結果的程式，其中包含一些基本的性質分析，也包含有別於其他分析軟體的性質分析。然而，由於程式運作於Linux指令模式下，新進的人員學習不易，另外，有經驗的使用者也會出現忘記指令、打錯指令等情形，而近年來由於網際網路發展與普及，在科學領域上有許多基於網頁瀏覽器的運用，在這裡希望能藉助網際網路圖形化、互動性等優點，解決前述提到的問題。 本實驗室透過建置維基網站，以及自行研發的網頁介面軟體 Pine-MD Graphical User Interface (Pine-MD GUI) 嘗試解決上述問題並整合資源。藉由實驗室維基網站的建立，將Pine-MD的指令與格式作有系統的整合，藉由維基共筆的特性，將有助於程式的更新與發展。而Pine-MD GUI是一套用來輔助Pine-MD的網頁介面軟體，使用者可以直接透過點選的方式輸入Pine-MD指令取代原本手動編輯的不便，而不論是實驗室的維基網站或是Pine-MD GUI，都希望能透過網頁的方式更有效率的進行科學的研究。 利用Pine-MD GUI網站架構，我們分析細菌膜在Na+, Mg2+ 及Ca2+ 陽離子存在下，膜微觀性質的變化，發現在Ca2+ 對細菌膜的影響有別於Na+及 Mg2+ 離子: Ca2+ 使得細菌膜結構更為緊實且主要分佈於磷脂質的磷酸基團附近。 Pine-MD (Protein INformation Extraction from Molecular Dynamics Simulation) is an in-house program designed to analyze the results of molecular dynamics simulations. It capcitity includes the analysis of molecular geometry, molecular conformation, inter-molecular structure, configuration, structure comparsion and classification, membrane properties, time-correlation property and statistics. This program uses text-based commands working under Linux environment, which is not user-friendly. Taking the fast development of web-based techniques, we setup a Lab Wiki and designed a program called Pine-MD GUI interacfacing with Pine-MD to integrate research resource and to assist the analysis of MD simulations. With the aid of Lab Wiki, lab researchers can access the detailed and updated commands and methods of Pine-MD through the internet everywhere. Moreover, the program developers can easily update the commands and methods of their newly develpoed programs through Lab Wiki. Pine-MD GUI is a newly developed program interfacing with Pine-MD working through Intenet browser. Pine-MD GUI has the following features making it user friendly: Its graphical interface reduced the text-command inputs by users; it guides users step-by-step for analysis which decreased the learning time of new users; in particular, its pop-up menu allows users to do atom section directly and friendly without any mistake. It improves the molecular simulation research effectively. Using Pine-MD GUI, we analyze the miscroscopic properties of model bacterial membranes under Na+, Mg2+ and Ca2+ environments obtained from all-atom MD simulations. Results show that member under Ca2+ ion environments is packed more order that those of other two ions. Interestingly, Ca2+ ions prefer to locate around the phosphate groups different from those of other two ions.
