Haptic Rendering of Molecular Conformations

Abstract

Current computational simulation are capable of producing enromous amounts of data. Complete understanding of their features presents a challenge even if very sophisticated visualization techniques are deployed. Computational analysis of conformational behaviour of biologically active compounds represents such simulation. We investigate methods how haptic rendering may contribute to better and faster understanding of the simulation results. This paper presents current progress in our research. I. Molecular Flexibility and Conformational Behaviour Many molecules exhibit an important chemical property --- flexibility. Biological activity of large molecules is directly related to their flexibility. The flexibility can be described in terms of conformational behaviour of the molecule. Undergoing the behaviour, the molecule changes its shape (config- uration) only, no chemical bonds are either created or broken, as well as the absolute configuration on atoms (or other chiral centres) does not change. Roughly speaking, internal potential energy of the molecule is a function of the configuration, therefore, in general, not all the configurations are favoured equally. By conformations we mean local potential energy minima, i. e. the configurations that are more stable than the others. Then the conformational behaviour is the process of traversing among conformations via transition states