Figure 2

Routine pipe-line for structural bioinformatics analysis of protein phosphorylated states. Once the protein is identified, a sequence-based search (1) in the Protein Data Bank (http://www.rcsb.org/pdb) structure database is done to download a 3D structure suitable to be used in computational simulation studies. In the case that the protein is not present in the database, bioinformatics modelling methods are used to generate an approximate model of the desired structures (2). Next step consists of the generation of the 3D model for the single protein or the interacting pair of proteins both in the unphosphorylated (basal) or the phosphorylated states (3). Finally, a Molecular Dynamics approach is used to compare the behaviour of the two states. RMSD (root mean square distance) values are collected for several nanoseconds in order to obtain a quantitative measure of the differences (4).