Reconstruction of the 3D coordinates of alpha-carbon atoms of proteins from a pair of stereographic figures.

In an attempt to promptly use the experimentally determined structures of proteins in modeling studies, we have developed the program ReconstC alpha to generate the 3D coordinates of alpha-carbon atoms from a pair of stereographic figures. Calculations of the 3D coordinates were performed by estimating the stereo parameters systematically. Geometrical features of C alpha traces were used to evaluate the integrity of the calculated structure. The program was applied to four kinds of protein structures to examine the performance. It was found that the root-mean-square deviation of atomic positions between constructed and reference crystal structures ranged from 0.36 to 0.78 A. The range represents a reasonable accuracy and its automatic feature suggests that our approach would be expedient for providing initial structures for protein modeling studies.