- COSMOsim 生命科學軟體
介紹The COSMO-RS method has proven the σ-profiles as the crucial information for most ADME properties as solubility, blood-brain-partition coefficients, and intestinal absorption, and even for many adsorption phenomena. Considering this fundamental importance of the σ-profiles for surface interactions of molecules in liquid states, they most likely also carry a large part of information required for the estimation of desolvation and binding processes, which are responsible for the inhibition of enzyme receptors by drug molecules. Thus a high similarity with respect to the σ-profiles appears to be
Driven by this insight, we have developed a σ-profile based drug similarity measure SMS for the detection of new bioisosteric drug candidates, and a program, COSMOsim, which enables the efficient calculation of this similarity for large libraries, making use of our COSMOfragtechnology. In several examples COSMOsim has already demonstrated its statistical and pharmaceutical plausibility, its practicability for real drug research projects, and its unique independence from the chemical structure which enables scaffold hopping in a natural way.
Despite these initial successes, which clearly proof the significance of the σ-profile similarity for drug similarity and bioisoster screening, we are aware that high SMS similarity cannot be a sufficient condition for drug activity, because no 3D-information is included in this measure. More refined methods combining 3D aspects and SMS similarity are under development – partly in academic collaborations – and will be added to our COSMOsim program during the next one or two years. Nevertheless, even in its present early development stage, COSMOsim should open a novel view to drug similarity, and provide many new and complementary ideas compared to the conventional more structure based similarity search methods.
MOPAC2009™ is the successor to a MOPAC2007™, a semiempirical quantum chemistry software package for the prediction of chemical properties and modeling of chemical reactions. It is used by chemists and biochemists for both research and teaching, and runs on Windows®, Linux and Macintosh platforms.
Turbomole被認為是進行HF，DFT，MP2計算最快最穩定的代碼之一。它的特色不是在於新方法和新功能，而在於解決如何用盡量短的時間和 盡量少的內存需求，快速、穩定地處理工業應用型的分子。特別是它獨有的RI-DFT方法，據稱可以較其它大多數DFT程序節省10倍的CPU時間，因此非 常適合於大分子計算或中等分子的重複性計算（如幾何優化）