Protein binding prediction using non-metric multidimensional scaling method

Protein-protein interaction is very important biological process. Individual proteins can form complex to function or can bind to others to recognize them, e.g. in immunological systems. In spite of that, it is unclear how they bind to each other. In other word, it is unclear which parts of protein can act as protein-protein binding sites. In this paper, we propose usage of non-metric multidimensional scaling method to align protein complexes structurally before investigating protein-protein binding site. It can align pair of proteins with deformation such that root mean square distance is minimized.