Pathway of the conformational transitions in flexible molecules

The pathways of the conformational transitions in flexible molecular systems were studied by the DDRP (Dynamically Determined Reaction Path) method implemented in TINKER molecular modelling package. Our first model systems were conformational transitions in small organic molecules (determination of rotational transitions, boat-chair transitions, etc.). The method was found to be very effective in finding such transitions and the location of the transition state. In comparison with other methods (modified Elber and Czerminski (EC) method implemented also in TINKER), similar results were obtained. For the conformational change of di- and small peptide fragments also acceptable paths and barriers were obtained. To determine the conformational transition in large peptides (i.e. folding), the effectivity of the procedure demands further studies. (c) 2005 Elsevier B.V. All rights reserved.