Betancourt M R, Skolnick J
Laboratory of Computational Genomics, The Donald Danforth Plant Science Center, 893 N. Warson Rd., Creve Coeur, MO 63141, USA.
Biopolymers. 2001 Oct 15;59(5):305-9. doi: 10.1002/1097-0282(20011015)59:5<305::AID-BIP1027>3.0.CO;2-6.
We introduce a new variant of the root mean square distance (RMSD) for comparing protein structures whose range of values is independent of protein size. This new dimensionless measure (relative RMSD, or RRMSD) is zero between identical structures and one between structures that are as globally dissimilar as an average pair of random polypeptides of respective sizes. The RRMSD probability distribution between random polypeptides converges to a universal curve as the chain length increases. The correlation coefficients between aligned random structures are computed as a function of polypeptide size showing two characteristic lengths of 4.7 and 37 residues. These lengths mark the separation between phases of different structural order between native protein fragments. The implications for threading are discussed.
我们引入了一种均方根距离（RMSD）的新变体，用于比较蛋白质结构，其取值范围与蛋白质大小无关。这种新的无量纲度量（相对RMSD，或RRMSD）在相同结构之间为零，而在与相应大小的平均一对随机多肽一样全局不同的结构之间为一。随着链长增加，随机多肽之间的RRMSD概率分布收敛到一条通用曲线。对齐的随机结构之间的相关系数作为多肽大小的函数进行计算，显示出4.7和37个残基的两个特征长度。这些长度标志着天然蛋白质片段不同结构顺序阶段之间的分隔。讨论了其对穿线法的影响。
