Large scale conformational rearrangements represent both a challenge and an opportunity for rational drug design. Exploring the conformational space of a target protein with sufficient detail is computationally very demanding and most current docking programs are very limited in this respect. If it were possible, however, it could open the avenue to the design of more selective drug candidates. Here we show how atomistic molecular dynamics together with methods developed to accelerate rare events can be used to study both kinase conformational transitions and ligand binding. Using a new sampling method which is able to find the low free energy channel between an initial and final state[1] we determined the atomistic dynamics of the open-to-closed movement of the cyclin dependent kinase 5 (CDK5). [4] The inactivation movement has a two-step mechanism. First alpha-C-helix rotates about 45 allowing the interaction between Glu51 and Arg149, then T-loop has to refold to assume the closed conformation. We found out the key role of Arg149 in the closure movement as the link residue between the N-lobe and the C-lobe, allowing a concerted movement of the two lobes. We do not find evidence for the DFG out flip. A complementary method, Metadynamics,[2,3] was used to study the undocking path of a congeneric series of ligands to CDK2. Also in this case the large scale dynamics of the kinase plays a fundamental role. 1. D. Branduardi, F. L. Gervasio and M. Parrinello. Rare events in molecular systems: From A to B in Free Energy Space J. Chem. Phys., 126, 054103, 2007. 2. F. L. Gervasio*, A. Laio and M. Parrinello. Flexible Docking in Solution Using Metadynamics J. Am. Chem. Soc., 127(8): 2600-2607, 2005. 3. A. Laio and F. L. Gervasio* Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science Rep. Prog. Phys. , 71, 126601 (22p), 2008. 4. A. Berteotti, A. Cavalli, D. Branduardi, F. L. Gervasio*, M. Recanatini and M. Parrinello, Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations nism of CDK5. J. Am. Chem. Soc.,131, 244-250, 2009.