Model scenarios for the understanding of molecular recognition

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Abstract
There are many factors (energetic, entropic, and kinetic) which have to be taken into account within a theoretical concept for molecular recognition. In this paper a model scenario is presented in which these different components are transferred to a representation for which human pattem recognition abilities can be used. It is demonstrated in particular that the van der Waals surface of molecules can be used as a screen for the representation of information pattern (electrostatics, local hydrophobicity, surface topography, molecular flexibility, etc.) which are relevant in molecular recognition processes. The technology of modem graphics workstations allows us to "see" a molecular scenario from the point of view of a molecule and to interact with this virtual world in a natural way. It is shown that this interaction with simulated molecular reality is not restricted to a local computational environment. New network communication techniques can be used to provide chemistry related information. A new approach is based on the virtual reality modelling language (VRML) which extends the world wide web (www> interface to visualize three dimensional (3D) scenarios and interact with the basic elements. It is demonstrated that the human recognition abilities can be transferred, at least partly, to a formal algorithmic concept by using fuzzy logic.

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