The thematic unit V (items 13 to 14) describes the general application of modeling techniques to the discovery of new molecules, engineering and design of proteins, function prediction, the interaction between two or more proteins. We review the basic principles of protein design and major modifications that can be performed on proteins known to improve or change their properties (stability, activity, etc..). It then proceeds to the description of receptor ligand interactions and how to take advantage of interaction models generated to predict protein function. Most models that include protein-protein interactions can be used to predict protein sequences capable of interacting with the model. Once found you can do a search on a set of genes or the entire genome of the organism of interest and identify potential targets. The identification of interactions based on structure opens the door to pharmacological intervention by direct competition molecules or small peptides with binding site described in the model. Furthermore the method is generalized search for genomic level function, and it extends to any type of receptor or ligand protein. Following, the methods to apply theoretical energy calculations and complex models to determine the energy and interaction energy stability are explained. It is addressed the systems biology, since proteins do not function in isolation, but work through complex interactions, protein-protein, protein-ligand and protein solvent. It describes major sources of information systems biology, such as the microarray and proteomics and how information is integrated to give a model, like the human immune system, which will be described in detail. The directed evolution of proteins also receives special attention, studying the tolerance of the host protein amino acid substitutions. It also describes the most commonly used experimental techniques virtual scanning to discover protein function, such as two-hybrid and phage display. To finish the program it is discusses the molecular design of biological materials designed by nature: new scaffolds, biominerals, adhesives and fluorescent materials that can serve as reference to create new molecules with modified functions. They show methods for rational design of self-assembled short peptide sequences and its application to biomedical engineering research or biotech or nanotech.