Projection of molecular interaction possibilities onto a cylinder surface

Abstract

A method is presented to depict the interaction possibilities of a molecule by projecting the van der Waals envelope and the electrostatic potential onto a cylinder surface. Unfolding of the cylinder allows the viewing of the molecule from all sides simultaneously, thus rendering unnecessary multiple representations from different viewing angles. The comparison of similar molecules, e.g. mimics, is thus greatly simplified. Qualitative representations and quantitative expressions for differences between molecules are easily derived from the procedure. The method should be especially useful in cases where the entire van der Waals surface is expected to be in contact with a complexation site, i.e. where interacting molecules are surrounded entirely by their binding site, e.g. in enzymes, cyclodextrins or polymer matrices. Molecule structure files are included on disk.