Development of a System of Simulation Biopolymer Systems in Dihedral Angle Space

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During the last ten or more years we have been developing a system of computation and a software system to implement the computation for simulation of conformations of biopolymer systems in the dihedral angle space. The purpose of this project is (a) to expand the scope of this computation and (b) to prepare for making it available for world-wide users. As to these purposes we have attained the following results. (1) The system of software has been reformulated according to the intrinsic logic which the algorithm contains inherently. Accordingly the system attained a generality and flexibility. A paper describing this reformulation is in press in Computer Physics Communication. (2) The system of computation in the dihedral angle space has proved very successful as applied for proteins. However, successful application for nucleic acids has been hampered by the flexibilities of the five-memebered ribose and deoxyribose rings. In order to overcome this difficulty, an analytic theory to treat pseudo-rotation of ribose and deoxyribose rings has to be developed. We have succeeded to give a fundamental solution to this problem. A peper describing this theory has been published in J.Phys.Chem. (3) We have developed a system of computation for treating nucleic acids by incorporating the above method of treating the pseudo-rotation of the five-membered rings. To be more specific, we have developed an algorithm to deduce three dimensional strucutres of nucleic acids from distance information obtainable from experimental NMR information. This algorithm allows to treat accurately the flexibities of ribose and deoxyribose rings. This algorithm is not only faster but also less biased than the now popular algorithm that works in the Cartesian coordinate space.