1.請詳讀SPYRAL資料夾中 Install.txt
CombiGlide結合了準確的配體-受體打分，巧妙的組合對接算法，和高效的內核切換技術，用
於設計重點的數據庫和辨認新的蛋白骨架。Desmond用於對生物分子體系進行高效的分子動力
學模擬。Desmond對速度和精度的平衡使得它可以用分子動力學模擬長時間標度的分子，甚至
用來檢測具有生物學和藥學意義的事件。Epik可以快速準確地預測pKa。Glide提供了完整的
配體-受體對接求解方案。Jaguar是著名的密度泛函和從頭量子化學計算程式。KNIME Extens
ions使用著名的開源KNIME介面，用於自動生成流程圖和進行數據分析。Liaison可以高效準確
地預測配體-受體的結合自由能。LigPrep產生準確的3D分子模型。MacroModel結合了領先的力
場（MM2，MM3，AMBER，AMBER94，MMFF，OPLS，MMFFs，OPLS-AA），準確高效的有效溶劑模型
，以及高級的構象搜索方法，提供了最完整的分子模擬程式套件。Maestro是強大的多用途的
分子模擬圖形環境，學術用戶可以免費申請使用。Phase是高效率的配體藥物設計程式。Prime
用於準確預測蛋白質結構。PrimeX使用OPLS-AA力場，用於準確預測蛋白質晶體結構。QikProp
可以快速預測可能的藥物。QSite是QM/MM程式，QM區的計算使用Jaguar，可以用Hartree-Fock
，DFT，或局域MP2方法求解。SiteMap是快速準確的結合位識別程式。Strike是強大的統計模
擬和QSAR程式。
Schrodinger is a suite of molecular modeling packages that take advantage
of the latest technological advances in computational chemistry. Jaguar,
the high-performance ab-initio quantum mechanics application, and
MacroModel, the most trusted name in molecular modeling, have been widely
applied to address the full range of chemical research from materials to
life sciences. Strike is a chemically aware statistical package for
examining structure-property relationships. QSite is a powerful QM/MM
application for studying reaction mechanisms in a variety of systems,
such as protein active sites.
Also, Schrodinger provides a complete suite of software that addresses
the challenges in pharmaceutical research. For structure-based drug
design, Prime is an accurate protein structure prediction package;
Glide performs accurate, rapid ligand-receptor docking; and Liaison
predicts binding affinity. Schrodinger also provides Phase for ligand-based
pharmacophore modeling, and QikProp for ADME properties prediction of drug
candidates. In addition, LigPrep is a rapid 2D to 3D conversion program
that can prepare ligand libraries for further computational analyses.
And most recently, Schrodinger introduced CombiGlide for focused library
design, and Epik for accurate enumeration of ligand protonation states in
biological conditions. Finally, Maestro is the graphical user interface
for all of Schrodinger's computational programs and provides a powerful,
fully-integrated molecular visualization and analysis environment.
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