Ab inition folding
Problem: The program is intended for calculating 3D structure of proteins, provided that 3D structures of individual parts (fragments) of the protein are known, while phi and psi angles between the fragments should be found. This problem may arise when constructing a protein structure from fragments, whose structures were obtained using the search for homology of their primary sequences
Method: The angles are calculated by genetic algorithm. The target optimization function is comprised by two additive contributions: (a) energy of the short-range interaction between the fragments and (b) the energy of phi/psi angles constructed basing on statistics of the angles between fragments of secondary structures in protein 3D structures from PDB database.
Results: Testing using seven natural proteins (with lengths from 58 to 135 aa; each protein consisted of several fragments) demonstrated that the program restores the native structure with a mean accuracy of 126.96.36.199 A. The prediction accuracy depends on individual protein and program operation mode: for three best proteins, the mean value of RMSD between the restored and native structures over ten runs amounted to 1.9, 2.3, and 2.6 A.
Program is provided with viewer.