Liu X-S, Guo W-L
Institute of Nanoscience, Academy of Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.
Amino Acids. 2008 May;34(4):643-52. doi: 10.1007/s00726-007-0017-2. Epub 2008 Jan 4.
Measuring residue conservation at aligned positions has many applications in biology. Recently, a new conservation score has been defined. Unlike the previous methods, the new approach considers both residue frequencies and physicochemistries. Specifically, it measures physicochemistries based on BLOSUM matrices disregarding the meaning of the entries in such matrices, which may involve the problem of log-log probability. In this paper we present a conservation measure that also reflects both frequencies and physicochemistries while considering the fact that the entries of BLOSUM matrices are already interpreted as log probability. When the supposed score is applied to 14 protein examples, the results show that these two conservation scores are equivalent aside from the different score ranges. The method is also used to score the functional sites of three protein families. Compared with the widely used entropy-based methods, the resulting scores are more robust and consistent in the sense that the functional sites are much more conserved because of functional constraints.
测量比对位置上的残基保守性在生物学中有许多应用。最近，定义了一种新的保守性得分。与先前的方法不同，新方法同时考虑了残基频率和物理化学性质。具体而言，它基于BLOSUM矩阵测量物理化学性质，而不考虑此类矩阵中条目的含义，这可能涉及对数-对数概率的问题。在本文中，我们提出了一种保守性度量方法，该方法在考虑到BLOSUM矩阵的条目已被解释为对数概率这一事实的同时，也反映了频率和物理化学性质。当将假定的得分应用于14个蛋白质实例时，结果表明，除了得分范围不同外，这两种保守性得分是等效的。该方法还用于对三个蛋白质家族的功能位点进行评分。与广泛使用的基于熵的方法相比，所得分数在功能位点因功能限制而更加保守的意义上更加稳健和一致。
