第六讲 蛋白质基本本质的表明2016秋.pptVIP

* Chou-Fasman Limitations: This algorithm is statistical; that is, it looks at the probability that a given protein exists in a given secondary structure element. Inaccuracies can arise if your protein sequences is substantially dissimilar from test case proteins and test case protein families. Chou predict 80% accuracy in assigning secondary structure using the 64 protein method. * 二级结构预测(5)： PSIPRED 生物信息学网站（http://bioinf.cs.ucl.ac.uk/psipred/）提供的基于神经网络搜索工具PSI-BLAST的PSIPRED蛋白二级结构预测方法，结果返回到学术性（商业后缀的信箱不可用）的Email信箱。 * 二级结构预测(5)： PSIPRED 生物信息学网站（http://bioinf.cs.ucl.ac.uk/psipred/）提供的基于神经网络搜索工具PSI-BLAST的PSIPRED蛋白二级结构预测方法，结果返回到学术性（商业后缀的信箱需申请密码）的Email信箱 * PSIPRED 参考文献 * PSIPREDhttp://bioinf.cs.ucl.ac.uk/psipred/ * Hydropathy: Goldman-Engleman-Steitz 该方法是使用Goldman, Engleman and Steitz (1986)模型对可能穿越细胞膜的非极性α-螺旋进行预测。非极性螺旋的搜索是根据蛋白质序列上氨基酸残基极性指数进行的。极性指数则是根据非极性双层脂膜区域与待考察残基相互作用的程度得到的。出于自由能的考虑，该方法不考虑卷曲和β-折叠的类型，因为这样的结构是不可能由细胞质插入到双层脂膜中的。基于残基的亲水和疏水成分以及位于α-螺旋上的每一个残基的表面区域，赋于每个氨基酸的跨膜自由能值。因此，这种方法用于预测跨膜螺旋结构比只根据残基亲疏水性指数来判断的方法来得准确。 * Goldman-Engleman-Steitz Parameters: The only parameter is how many Residues to Average when constructing each point in the plot. The default is 20, to reflect a common transmembrane alpha helix. Factors playing into the choice of window length are the hydrophobic length of the bilayer and the orientation of a potential helix within it. 21 residues are required to span a lipid bilayer 30? long, as the interval between residues in an a-helix is 1.5?. Limitations: This algorithm is much more accurate at predicting membrane bound helices than other hydropathy methods, especially if the helix contains polar residues. It makes no attempt at predicting other structural elements and would not be accurate for non-helical membrane bound structures. Non-helical membrane bound structures are not very common, due to the high free energy costs of folding in a polar environment and functioning in a non-polar environment. * Hydropathy: Kyte-Doolittle Kyte and Doolittle (1