Richa Tambi, Ide Soichiro, Suzuki Ryosuke, Ebina Teppei, Kuroda Yutaka
Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 12-24-16 Nakamachi, Koganei-shi, Tokyo, 184-8588, Japan.
Department of Physiology, Graduate school of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
J Comput Aided Mol Des. 2017 Feb;31(2):237-244. doi: 10.1007/s10822-016-9999-8. Epub 2016 Dec 27.
Efficient and rapid prediction of domain regions from amino acid sequence information alone is often required for swift structural and functional characterization of large multi-domain proteins. Here we introduce Fast H-DROP, a thirty times accelerated version of our previously reported H-DROP (Helical Domain linker pRediction using OPtimal features), which is unique in specifically predicting helical domain linkers (boundaries). Fast H-DROP, analogously to H-DROP, uses optimum features selected from a set of 3000 ones by combining a random forest and a stepwise feature selection protocol. We reduced the computational time from 8.5 min per sequence in H-DROP to 14 s per sequence in Fast H-DROP on an 8 Xeon processor Linux server by using SWISS-PROT instead of Genbank non-redundant (nr) database for generating the PSSMs. The sensitivity and precision of Fast H-DROP assessed by cross-validation were 33.7 and 36.2%, which were merely ~2% lower than that of H-DROP. The reduced computational time of Fast H-DROP, without affecting prediction performances, makes it more interactive and user-friendly. Fast H-DROP and H-DROP are freely available from http://domserv.lab.tuat.ac.jp/ .
仅根据氨基酸序列信息高效快速地预测结构域区域，对于大型多结构域蛋白质的快速结构和功能表征通常是必需的。在此，我们介绍Fast H-DROP，它是我们之前报道的H-DROP（使用最优特征预测螺旋结构域连接子）的加速30倍版本，其独特之处在于专门预测螺旋结构域连接子（边界）。与H-DROP类似，Fast H-DROP通过结合随机森林和逐步特征选择协议，使用从3000个特征中选出的最优特征。通过使用SWISS-PROT而非Genbank非冗余（nr）数据库来生成位置特异性得分矩阵（PSSM），我们在8个至强处理器的Linux服务器上，将计算时间从H-DROP中每个序列8.5分钟减少到Fast H-DROP中的每个序列14秒。通过交叉验证评估，Fast H-DROP的灵敏度和精确率分别为33.7%和36.2%，仅比H-DROP低约2%。Fast H-DROP在不影响预测性能的情况下减少了计算时间，使其更具交互性和用户友好性。Fast H-DROP和H-DROP可从http://domserv.lab.tuat.ac.jp/免费获取。
