Tyagi Manoj, Bornot Aurélie, Offmann Bernard, de Brevern Alexandre G
Laboratoire de Biochimie et Génétique Moléculaire, Université de La Réunion, BP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France.
Comput Biol Chem. 2009 Aug;33(4):329-33. doi: 10.1016/j.compbiolchem.2009.06.002. Epub 2009 Jun 25.
Loops connect regular secondary structures. In many instances, they are known to play crucial biological roles. To bypass the limitation of secondary structure description, we previously defined a structural alphabet composed of 16 structural prototypes, called Protein Blocks (PBs). It leads to an accurate description of every region of 3D protein backbones and has been used in local structure prediction. In the present study, we used our structural alphabet to predict the loops connecting two repetitive structures. Thus, we showed interest to take into account the flanking regions, leading to prediction rate improvement up to 19.8%, but we also underline the sensitivity of such an approach. This research can be used to propose different structures for the loops and to probe and sample their flexibility. It is a useful tool for ab initio loop prediction and leads to insights into flexible docking approach.
环连接规则的二级结构。在许多情况下，已知它们发挥着关键的生物学作用。为了绕过二级结构描述的局限性，我们之前定义了一个由16种结构原型组成的结构字母表，称为蛋白质模块（PBs）。它能准确描述三维蛋白质主链的每个区域，并已用于局部结构预测。在本研究中，我们使用我们的结构字母表来预测连接两个重复结构的环。因此，我们发现考虑侧翼区域很有意义，这使得预测率提高了19.8%，但我们也强调了这种方法的敏感性。这项研究可用于为环提出不同的结构，并探测和采样它们的灵活性。它是从头预测环的有用工具，并有助于深入了解灵活对接方法。
