双绕蛋白质的分类与识别  

Classification and recognition of Rossmann-fold protein

作　　者：刘岳[1] 徐海松[1] 乔辉[1] 李晓琴[1] 

机构地区：[1]北京工业大学生命科学与生物工程学院,北京100124

出　　处：《生物信息学》2010年第1期1-6,共6页Chinese Journal of Bioinformatics

基　　金：国家自然科学基金(30570427);北京市自然科学基金(4063035)资助项目

摘　　要：蛋白质折叠识别是蛋白质结构研究的重要内容。双绕是α/β蛋白质中结构典型的常见折叠类型。选取22个家族中序列一致性小于25%的79个典型双绕蛋白质作为训练集,以RMSD为指标进行系统聚类,并对各类建立基于结构比对的概形隐马尔科夫模型(profile-HMM)。将Astral1.65中序列一致性小于95%的9 505个样本作为检验集,整体识别敏感性为93.9%,特异性为82.1%,MCC值为0.876。结果表明:对于成员较多,无法建立统一模型的折叠类型,分类建模可以实现较高准确率的识别。Fold recognition is an important issue in protein structure research.The Rossmann-fold protein that has typical structure is a common kind of α/β protein.The training set,selected from 22 families,is constituted of 79 Rossmann-fold proteins which have less than 25% sequence identity with each other.The hierarchical clustering method according to RMSD is applied and a profile-HMM based on structure alignment is built for each cluster.Testing on 9 505 proteins with less than 95% sequence identity from Astral1.65,the sensitivity,specificity and MCC are 93.9%,82.1% and 0.876 respectively.The result shows that building profile-HMMs after classification could reach precise fold recognition while a unified one cannot be built due to there are too many members in training set.

关 键 词：双绕蛋白质 RMSD 系统聚类 隐马尔科夫模型 折叠类型识别 

分 类 号：Q523[生物学—生物化学]