Fast protein fold recognition via sequence to structure alignment and contact capacity potentials.
Fast protein fold recognition via sequence to structure alignment and contact capacity potentials.
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发表时间：
1996
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通讯作者：
PotentialsbyNickolai N. Alexandrov;R. Nussinov;Ralf M. Zimmer
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作者：
PotentialsbyNickolai N. Alexandrov;R. Nussinov;Ralf M. Zimmer
我们提出了新的经验评分潜力和相关的最佳比对蛋白质序列的蛋白质结构的比对程序。该方法有两个主要的应用：第一，一个合理的折叠识别未知结构的蛋白质序列的数据库中的代表性蛋白质结构，第二，序列比对的改进，通过使用结构信息，以找到一个更好的起点同源性为基础的建模。的经验得分函数是来自一个非冗余的数据库的已知结构的分析，通过转换成伪能量使用的归一化根据逆Bolzmann定律的相对频率。这些所谓的接触电容电位被证明是足够的区别性，以检测结构折叠的情况下，显着的序列相似性，并在同一时间足够简单，以允许一个非常快速的优化比对程序。
We propose new empirical scoring potentials and associated alignment procedures for optimally aligning protein sequences to protein structures. The method has two main applications: first, the recognition of a plausible fold for a protein sequence of unknown structure out of a database of representative protein structures and, second, the improvement of sequence alignments by using structural information in order to find a better starting point for homology based modelling. The empirical scoring function is derived from an analysis of a nonredundant database of known structures by converting relative frequencies into pseudoenergies using a normalization according to the inverse Bolzmann law. These-so called contact capacity-potentials turn out to be discriminative enough to detect structural folds in the absence of significant sequence similarity and at the same time simple enough to allow for a very fast optimization in an alignment procedure.