Block-units method for conformational calculations of large nucleic acid chains. II, The two-hierarchical approach and its application to conformational arrangement of the unusual TψC loop of rabbit tRNA val

The two‐level hierarchical methodology is suggested for conformational calculations of large fragments of nucleic acids. The method of the first level is intended for performing a fast screening of the conformational phase space. The high‐level method may be used to refine structurally important conformations. The method of the first level is the block‐units method, which has been developed specially for these purposes (see part I). It has been shown that the block‐units method allows the satisfactory calculation of the structure parameters of the optimal conformations of polynucleotides. The results of the conformational rerrangement calculations of the TψC loop of the tRNA Phe after modification of its sequence are represented.