Search Strategies, Minimization Algorithms, and Molecular Dynamics Simulations for Exploring Conformational Spaces of Nucleic Acids

We describe recent computational strategies employed in our nucleic acid programs DUPLEX (in dihedral angle space) and MADPAC (in cartesian space). Under the first category of Search Strategies, we discuss: i) a build-up technique for nucleic acids, ii) the use of "soft" constraints to locate structures that match NMR data or to locate specific hydrogen-bonding patterns, and iii) a helix generator for single and double-stranded RNA and DNA. In the second category of Minimization, we describe a rapidly convergent truncated Newton method specifically adapted for potential energy functions. Third, in the category of Molecular Dynamics, we introduce a new algorithm based on the Langevin equation and the implicit Euler Scheme. The implicit formulation relaxes the severe restriction on the time step size (as in explicit schemes) and, furthermore, allows incorporation of a "cutoff" frequency c which effectively freezes modes of much higher frequency than c.

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