Some Methods for Examining the Interactions between Two Molecules

When studying the interaction between two molecules, one needs to describe the interface to compare and contrast it with other systems. Three geometric methods for analyzing these interactions have been developed: (i) calculation of pairwise atomic contacts; (ii) calculation of surface area; (iii) calculation of packing volume. This paper describes these methods and focuses on the first two to describe antibody-antigen interactions. Application of these methods reveals some ways in which antibody interactions differ with different size antigens.