Chen Chien Peter, Rost Burkhard
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Protein Sci. 2002 Dec;11(12):2766-73. doi: 10.1110/ps.0214602.
Low-resolution experiments suggest that most membrane helices span over 17-25 residues and that most loops between two helices are longer than 15 residues. Both constraints have been used explicitly in the development of prediction methods. Here, we compared the largest possible sequence-unique data sets from high- and low-resolution experiments. For the high-resolution data, we found that only half of the helices fall into the expected length interval and that half of the loops were shorter than 10 residues. We compared the accuracy of detecting short loops and long helices for 28 advanced and simple prediction methods: All methods predicted short loops less accurately than longer ones. In particular, loops shorter than 7 residues appeared to be very difficult to detect by current methods. Similarly, all methods tended to be more accurate for longer than for shorter helices. However, helices with more than 32 residues were predicted less accurately than all other helices. Our findings may suggest particular strategies for improving predictions of membrane helices.
低分辨率实验表明，大多数膜螺旋跨越17至25个残基，并且两个螺旋之间的大多数环长于15个残基。这两个限制条件在预测方法的开发中都有明确应用。在此，我们比较了来自高分辨率和低分辨率实验的最大可能的序列唯一数据集。对于高分辨率数据，我们发现只有一半的螺旋落入预期的长度区间，并且一半的环比10个残基短。我们比较了28种先进和简单预测方法检测短环和长螺旋的准确性：所有方法预测短环比预测长环的准确性低。特别是，短于7个残基的环似乎很难被当前方法检测到。同样，所有方法对较长螺旋的预测往往比对较短螺旋更准确。然而，具有超过32个残基的螺旋的预测准确性低于所有其他螺旋。我们的发现可能为改进膜螺旋的预测提出特定策略。
