Figure 2

An example of the alignment for two protein chains 1DHF _a and 8DFR. The iteration number of the algorithm is represented by t. (a) The two proteins 1DHF _a and 8DFR are in the original coordinates, which are in the C _α representation of the backbone. (b) and (c) Relative positions of the two proteins during the convergence process. (d) The optimal alignment by our algorithm. The final alignment number m is 182 with rms = 0.7 at λ = 6.0 and $\overline{\lambda }$ = 0.0.