Burke D F, Deane C M
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB1 2GA, UK.
Protein Eng. 2001 Jul;14(7):473-8. doi: 10.1093/protein/14.7.473.
The SLoop database of supersecondary fragments, first described by Donate et al. (Protein Sci., 1996, 5, 2600-2616), contains protein loops, classified according to structural similarity. The database has recently been updated and currently contains over 10 000 loops up to 20 residues in length, which cluster into over 560 well populated classes. The database can be found at http://www-cryst.bioc.cam.ac.uk/~sloop. In this paper, we identify conserved structural features such as main chain conformation and hydrogen bonding. Using the original approach of Rufino and co-workers (1997), the correct structural class is predicted with the highest SLoop score for 35% of loops. This rises to 65% by considering the three highest scoring class predictions and to 75% in the top five scoring class predictions. Inclusion of residues from the neighbouring secondary structures and use of substitution tables derived using a reduced definition of secondary structure increase these prediction accuracies to 58, 78 and 85%, respectively. This suggests that capping residues can stabilize the loop conformation as well as that of the secondary structure. Further increases are achieved if only well-populated classes are considered in the prediction. These results correspond to an average loop root mean square deviation of between 0.4 and 2.6 A for loops up to five residues in length.
超二级结构片段的SLoop数据库由多纳特等人首次描述（《蛋白质科学》，1996年，第5卷，2600 - 2616页），包含根据结构相似性分类的蛋白质环。该数据库最近已更新，目前包含超过10000个长度达20个残基的环，这些环聚集成超过560个分布密集的类别。该数据库可在http://www - cryst.bioc.cam.ac.uk/~sloop找到。在本文中，我们识别出保守的结构特征，如主链构象和氢键。使用鲁菲诺及其同事（1997年）的原始方法，对于35%的环，预测出的正确结构类别具有最高的SLoop得分。通过考虑得分最高的三个结构类别预测，这一比例升至65%，而在得分最高的五个结构类别预测中则升至75%。纳入相邻二级结构的残基并使用基于二级结构简化定义得出的替换表，可将这些预测准确率分别提高到58%、78%和85%。这表明封端残基既能稳定环的构象，也能稳定二级结构的构象。如果在预测中仅考虑分布密集的类别，准确率会进一步提高。对于长度达五个残基的环，这些结果对应的平均环均方根偏差在0.4至2.6埃之间。
