Sugiyama Yoshiaki, Polulyakh Natalia, Shimizu Toshio
Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan.
Protein Eng. 2003 Jul;16(7):479-88. doi: 10.1093/protein/gzg068.
We propose a novel method for identifying and classifying the functions of transmembrane (TM) proteins based on their TM topology [the number of TM segments (tms), the loop length and the N-terminus location]. In this method, the TM topology is expressed as a string of '0' and '1', and this is designated the binary topology pattern (BTP). We focused on TM proteins with up to 12 tms, with the exception of 1 and 9 tms, and classified them into 37 functional groups by the number of tms and the functional annotation. These grouped TM protein sequences were used to determine BTPs which are specific to the individual functional groups. Since the evaluated accuracies (sensitivity, specificity and self-consistency) of these patterns in functional identification were quite high overall, i.e. 0.940, 0.934 and 0.935, respectively, as averaged over the 37 functional groups, we confirmed that TM protein function can be identified by the number of tms and the characteristics of loop lengths, i.e. BTPs.
我们提出了一种基于跨膜（TM）蛋白的跨膜拓扑结构[跨膜片段（tms）数量、环长度和N端位置]来识别和分类其功能的新方法。在该方法中，TM拓扑结构表示为一串“0”和“1”，这被称为二元拓扑模式（BTP）。我们关注的是tms数量最多为12个的TM蛋白，但不包括1个和9个tms的情况，并根据tms数量和功能注释将它们分为37个功能组。这些分组的TM蛋白序列用于确定各个功能组特有的BTP。由于这些模式在功能识别中的评估准确率（敏感性、特异性和自一致性）总体上相当高，即在37个功能组上平均分别为0.940、0.934和0.935，我们证实可以通过tms数量和环长度特征（即BTP）来识别TM蛋白的功能。
