Travelling through conformational space: an approach for analyzing the conformational behaviour of flexible molecules.

Abstract

The applications of the single-co-ordinate-driving (SCD) method in conformational analysis of flexible molecules have been discussed. SCD can best be characterised as travelling through low energy areas of the conformational space. It has been shown that SCD provides detailed information about the conformational behaviour of small and middle sized flexible molecules. It has been demonstrated that SCD may fail for molecules which are more rigid but still conformationally interesting, for example, AUG trimer of RNA. It has been found out that the search problems are eliminated when SCD is coupled with simulated annealing (SCD-SA). Both SCD and SCD-SA methods may be recognised as successful tools for analysis of conformational space. It has been demonstrated, how SCD and SCD-SA results can be used as a background to discover and analyse correlated conformational processes, to quantify molecular conformational flexibility, and to provide an appropriate background for an efficient free energy simulation.