DOI 10.1393/ncc/i2012-11335-1

Summary. — Optimization methods are a powerful tool in protein structure anal-ysis. In this paper we show that they can be profitably used to solve relevant problems in drug design such as the comparison and recognition of protein binding sites and the protein-peptide docking. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site whereas the search for correct protein-peptide docking is often based on the minimization of an interaction energy model. We show that continuous global optimization methods can be used to solve the above problems and show some computational results. PACS 02.70.-c – Computational techniques; simulations. PACS 02.60.Pn – Numerical optimization. PACS 87.15.bg – Tertiary structure