CirPred, the first structure modeling and linker design system for circularly permuted proteins

BMC Bioinformatics

Table 2 Effects of sequence identity on the performance of CirPred

Sequence identity^a (%)	Alignment ratio^b (%)	RMSD^b (Å)	Number of CP pairs
90–100	97.6	1.236	79
80–90	95.7	1.673	39
70–80	94.7	1.504	8
60–70	95.1	3.124	10
50–60	96.7	1.910	31
40–50	98.7	2.002	236
30–40	98.1	2.026	351
20–30	90.9	2.496	161
10–20	74.0	3.904	653

In this experiment, for each pair of circular permutants, one protein was utilized as the template to create the model of the other protein, i.e., the target
^aSequence identities between the template and target proteins
^bAlignment ratio and RMSD values between the model and known structure of target proteins

ISSN: 1471-2105